Type i interferon mimetics as therapeutics for cancer, viral infections, and multiple sclerosis

ABSTRACT

The subject invention pertains to agonist peptides of type I interferons and methods of using the peptides. These peptides are based on the amino acid sequence of the C-terminus region of the type I IFN molecules and are capable of binding to the cytoplasmic domain of type I IFN receptors. Surprisingly, these peptides were found to possess the same or similar biological activity as that associated with the full-length, mature type I IFN proteins, even though these peptides do not bind to the extracellular domain of the type I IFN receptors. In one embodiment, the peptide is a peptide of IFNα. In another embodiment, the peptide is a peptide of IFNβ. Exemplified peptides of the invention include those having SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ ID NO:39, and SEQ ID NO:40. The subject peptides have been shown to effect increased resistance to viral infection. Peptides of the invention can be used to treat or prevent viral infections, to treat oncological disorders, and to treat autoimmune disorders, such as multiple sclerosis.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation-in-part of InternationalApplication No. PCT/US2012/043565, filed Jun. 21, 2012, which claims thebenefit of U.S. Provisional Application Ser. No. 61/499,495, filed Jun.21, 2011, each of which is hereby incorporated by reference herein inits entirety, including any figures, tables, nucleic acid sequences,amino acid sequences, or drawings.

GOVERNMENT SUPPORT

This invention was made with government support under grant numberR01A1056152 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

The Sequence Listing for this application is labeled “2AT7634.TXT” whichwas created on Nov. 14, 2013 and is 21 KB. The entire contents of thesequence listing is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Viruses are a heterogeneous group of intracellular infectious agentsthat depend in varying degrees on the host synthetic machinery forreplication. The poxviruses are large, double-stranded DNA viruses thatare assembled in the cytoplasm of infected cells involving complexreplication mechanisms (Moss, 2007). Attachment, internalization, anddisassembling of poxviruses precedes the initiation of three waves ofmRNA synthesis. The early wave codes for virus growth factors and decoycytokine receptors. Decoy receptors for both type I and type IIinterferons (IFNs) are produced during early protein synthesis inpoxvirus infected cells, thus blunting perhaps the most important innatehost defense system against viral infections (Moss and Shisler, 2001). Awell-known example of this is the B8R protein of vaccinia virus, whichis a homolog of the extracellular domain of the IFNγ receptor (Moss,2007).

Encephalomyocarditis (EMC) virus is a small single-stranded RNApicornavirus of the plus strand orientation with wide host range(Racaniello, 2007). In mice, EMC virus infection is lethal, but is quitesusceptible to IFNγ or an IFNγ mimetic treatment at early stages ofinfection (Mujtaba et al., 2006). The IFNγ mimetic is also effectiveagainst vaccinia virus infection even in the presence of B8R decoyreceptor (Ahmed et al., 2005; Ahmed et al., 2007). The IFNγ mimetic is asmall peptide corresponding to the C-terminus of IFNγ that functionsintracellularly and thus does not interact with the extracellular domainof the IFNγ receptor (Ahmed et al., 2005).

The IFNγ mimetic is also effective against another large double-strandedDNA virus called herpes simplex 1 or HSV-1 that replicates in the cellnucleus (Frey et al., 2009). Close relatives include the herpes Zostervirus and cytomegalovirus (Roizman et al., 2007). The broad spectrum ofantiviral activity of IFNγ mimetics is unique in that we are unaware ofany other small antiviral that exhibits strong activity againstpoxviruses, picornaviruses, and herpes viruses.

The IFN system is regulated by an inducible endogenous tyrosine kinaseinhibitor called suppressor of cytokine signaling 1 or SOCS-1 (Yoshimuraet al., 2007; Mansell et al., 2006; Yasukawa et al., 1999; Kobayashi etal., 2006; Croker et al., 2008). SOCS-1 is a member of a family ofinducible proteins that negatively regulate IFN and other cytokinesignaling via inhibition of JAK/STAT signaling (Yoshimura et al., 2007).There are currently eight members of the SOCS family, SOCS-1 to SOCS-7and cytokine-inducible SH2 protein. SOCS-1 has distinct regions ordomains that define the mechanism by which it inhibits the function ofJAK tyrosine kinases such as JAK2 that are involved in activation ofSTAT transcription factors (Yoshimura et al., 2007). The N-terminus ofSOCS-1 contains a SH2 domain, and N-terminal to it is an extended SH2sequence (ESS) adjacent to a kinase inhibitory region (KIR) (Yoshimuraet al., 2007). These domains or regions of SOCS-1 bind to the activationand catalytic regions of JAK2 and block its function. The C-terminus ofSOCS-1 contains a domain called the SOCS box, which is involved inproteasomal degradation of JAK2. It has been shown that the KIR sequenceof SOCS-1 binds to a peptide corresponding to the activation loop ofJAK2, pJAK2(1001-1013), and that the peptide pJAK2(1001-1013) blockedSOCS-1 activity in cells (Waiboci et al., 2007). Specifically,pJAK2(1001-1013) enhances suboptimal IFN activity, blocks SOCS-1 inducedinhibition of STAT3 activation, enhances IFNγ activation site promoteractivity, and enhances antigen-specific proliferation.

Influenza A virus is a segmented negative strand RNA virus that isresponsible for over 30,000 deaths annually in the United States (Paleseand Shaw, 2007). Pandemic influenza A virus infection can cause thedeaths of millions world-wide. Type I IFNs are an important early innateimmune response cytokine against influenza respiratory infections(Szretter et al., 2009). Influenza virus-encoded nonstructural proteinNS1 is multifunctional and is important in virus defense against IFNs bya mechanism(s) that is not fully understood but may involve induction ofSOCS-1 and SOCS-3, which in turn would negatively regulate IFN signaling(Pothlichet et al., 2008).

Herpes Simplex Virus (HSV) is a member of a broad class ofdouble-stranded DNA viruses that undergo replication in the cellnucleus. Examples of other members are varicella-zoster virus (VZV) andcytomegalovirus (CMV) (Roizman et al., 2007). It is estimated that HSV-1infects 60 to 80 percent of the people throughout the world, andpersists for life in the infected individuals (Diefenbach et al., 2008;Koelle and Corey, 2008; Cunningham et al., 2006). Primary infectioncommonly occurs through cells of the mucous membrane and is oftenasymptomatic. This is followed by uptake of virus by sensory nervefibers and retrograde transport to the cell body of the neurons in thedorsal root or trigeminal ganglion. Here, acute infection is convertedto latency and from which HSV-1 periodically migrates down the nervetissue to again infect mucosal cells for overt disease (Roizman et al.,2007; Diefenbach et al., 2008; Koelle and Corey, 2008; Cunningham etal., 2006).

HSV-1 infection is characterized by a strong cytokine response ininfected cells, particularly the induction of type I IFNs (Cunningham etal., 2006). Infection of keratinocytes, for example, results ininduction of large amounts of IFNα and IFNβ as well as interleukins 1,6, and β-chemokines (Mikloska et al., 1998). IFNs, macrophages, naturalkiller (NK) cells, and gamma/delta T cells all play an important role inhost innate immune response to HSV-1 (Cunningham et al., 2006).Toll-like receptor (TLR) 2 is activated on the cell surface by HSV-1,while TLR-9 is activated intracellularly by viral DNA. The latterstimulus is thought to play an important role in induction of IFNα byHSV-1 (Cunningham et al., 2006).

The adaptive immune response plays an important role in confining HSV-1and other herpes virus infections to a latent state where CD8⁺ T cellsand IFNγ play critical roles (Knickelbein et al., 2008; Sheridan et al.,2007; Decman et al., 2005). It is functionally connected to the innateimmune system where NK cells can serve as a source of IFNγ, which isalso produced by CD4⁺ and CD 8⁺ T cells. IFNγ can exert direct antiviralactivity as well as induce upregulation of MHC class I and class IImolecules on macrophages, dendritic cells, and keratinocytes (Decman etal., 2005). Direct effects of IFNγ as per a mouse model suggest thatthis IFN prevents reactivation of HSV by inhibition of function of thekey intermediate protein ICP0 (Mossman, 2005). Interaction of theantigen presenting cells with CD4⁺ T cells induces CD8⁺ T cells tocontrol HSV-1 levels in mucosal lesions (Arduino and Porter, 2008; Patelet al., 2007).

HSV-1 has developed several mechanisms to inhibit both the innate andadaptive immune responses to infection. HSV-1 downregulation of class IMHC expression occurs through high affinity binding of viral immediateearly gene product ICP47 to the transporter associated with antigenprocessing (TAP) (Burgos et al., 2006), which blocks IFNγ induction ofcytotoxic CD8⁺ T cells (Goldsmith et al., 1998). IFN signaling is alsoinhibited by blockage of JAK/STAT transcription factor phosphorylationby an unknown mechanism (Chee and Roizman, 2004). ICP0 is thought toenhance proteasome-dependent degradation of IFN stimulated genes (ISGs)(Halford et al., 2006; Edison et al., 2002). A recent study suggeststhat HSV-1 can exert an anti-interferon effect by activation of aprotein called suppressor of cytokine signaling 3 (SOCS-3) (Yokota etal., 2004).

Currently, there are no effective therapeutics available against HSVinfection, except the nucleoside analog acyclovir (Dorsky andCrumpacker, 1987), which is known to have serious side effects. A searchfor a vaccine against HSV has remained elusive because of the successfuladaptation to the host used by HSV (Koelle and Corey, 2008). Along withdirect effects, infection with HSV has been found to increase theincidence of HIV infection, probably due to HSV-associated lesions (Waldand Link, 2002). Because of this interplay between HSV and HIV, it isconceivable that anti-HSV treatment may reduce the incidence ofinfection with HIV.

Type I interferons (IFNs), IFNα and IFNβ have been clinically approvedfor the treatment of hairy cell leukemia, chronic myelogenous leukemia,melanoma, hepatitis C virus infection, and multiple sclerosis. Treatmentwith these IFNs is associated with severe side effects, including bonemarrow suppression, depression, and fever, which has resulted in severalpatients dropping out of treatment programs. There remains a need in theart for type I IFN mimetics that can provide the same benefits as theparent interferons, while having less of the undesirable effects.

The classical model of cytokine signaling dominates our view of specificgene activation by cytokines such as the interferons (IFNs) (Levy andDarnell, 2002). In this model, ligand activates the cell solely viainteraction with the extracellular domain of the receptor complex. Thisin turn results in the activation of receptor or receptor-associatedtyrosine kinases, primarily of the Janus or JAK kinase family, leadingto phosphorylation and dimerization of the STAT transcription factors,which then disassociate from the receptor cytoplasmic domain andtranslocate to the nucleus. This view ascribes no further role to theligand, JAKs, or the receptor in the signaling process. Further, thereis the suggestion that the STAT transcription factors possess intrinsicnuclear localization sequences (NLSs) that are responsible for nucleartranslocation of STATs and specific gene activation (McBride et al.,2000; Melen et al., 2001; Begitt et al., 2000).

It has recently been acknowledged that the classical model of JAK/STATsignaling was over-simplified in its original form. In the case of IFNγ,complexity beyond simple JAK/STAT activation is indicated in therelatively recent demonstration that other pathways, including MAPkinase, PI3 kinase, CaM kinase II, NF-κB, and others cooperate with oract in parallel to JAK/STAT signaling to regulate IFNγ effects at thelevel of gene activation and cell phenotypes (Gough et al., 2008). Allof these pathways are generic in the sense that a plethora of cytokineswith functions different from those of IFNγ also activate them. Thus,uniqueness of function would seem to depend on cytokine control ofcomplex and unique qualitative, quantitative, and kinetic aspects ofactivation of these pathways. This uniqueness has thus far not beendemonstrated.

At the STAT level, there is evidence of a functional interaction betweendifferent STATs in gene activation/suppression, which provides moreinsight into STAT mediation of cytokine signaling. The induction ofIL-17 by activated STAT3, for example, was countered by IL-2 activationof STAT5 (Yang et al., 2011). It was demonstrated by chromatinimmunoprecipitation (ChIP) sequencing that STAT3 and STAT5 bound tomultiple common sites across the IL-17 gene locus, including non-codingsequences. The activation state of these STATs was not addressed.Induction of STAT5 by IL-2 resulted in more binding of STAT5 and lessbinding of STAT3 at these sites, whereas induction of STAT3 by IL-6induced the opposite; the combination of the two STATs resulted indynamic regulation of the IL-17 gene locus by the opposing effects ofIL-2 (STAT5) and IL-6 (STAT3) (Yang et al., 2011). A similarcomplementarity was observed with STAT4 and STAT6 with respect to Th1and Th2 cell development, but with much less competition for bindingsites at coding and non-coding regions of the gene (Wei et al., 2010).These Yin-Yang interactions of STAT transcriptions factors are referredto as specification with respect to lymphocyte phenotypes. It is notclear, however, as to how these STAT interactions at the level of DNAbinding translate into specific gene activation by the inducingcytokine.

There is evidence that JAK kinases, including the mutant JAK2V617F, playan important role in the epigenetics of gene activation in addition toSTAT activation in the cytoplasm (Dawson et al., 2009). Leukemic cellswith a JAK2V617F gain-of-function mutation have constitutively activeJAK2V617F in the nucleus. This leads to phosphorylation of Y41 onhistone H3, which results in disassociation of heterochromatin protein1α, HP1α. The heterochromatin remodeling was associated with exposure ofeuchromatin for gene activation. Although present in the nucleus,wild-type JAK2 was only activated when K562 cells were treated with PDGFor LIF, or when BaF3 cells were treated with IL-3. The question of how aligand/receptor interaction resulted in the presence of activated JAK2,pJAK2, in the nucleus was not addressed, nor its targeting mechanism todiscrete genomic sites and specific promoters.

It has been shown in the case of IFNγ that receptor subunit IFNGR1 isassociated with pJAK2 and phosphorylated histone H3Y41 at the promoterof the IRF1 gene, while the β-actin gene is unaffected, since it is notacted on by IFNγ (Noon-Song et al., 2011). Activated TYK2, pTYK2, in thenucleus and at promoters of genes activated by type I IFNs. TYK2 is alsoactivated by other cytokines such as IL-12 and IL-23, which havebiological effects different from IFN (Jones and Vignali, 2011; Duvalletet al., 2011). We were therefore particularly interested in whetherthere was an association between pTYK2 and type I IFN receptors at thepromoters and chromatin of genes activated by these IFNs and whethersuch association provided insight into pTYK2 induced specific epigeneticevents in genes activated by the IFNs. The findings provide insight intothe mechanism of specific gene activation by type I IFNs, including theassociated epigenetic events.

BRIEF SUMMARY OF THE INVENTION

The subject invention pertains to agonist peptides of type I interferonsand methods of using the peptides. These peptides are based on the aminoacid sequence of the C-terminus region of the type I IFN molecules andare capable of binding to the cytoplasmic domain of type I IFNreceptors. Surprisingly, these peptides were found to possess the sameor similar biological activity as that associated with the full-length,mature type I IFN proteins, even though these peptides do not bind tothe extracellular domain of the type I IFN receptors. In one embodiment,the peptide is a peptide of IFNα. In another embodiment, the peptide isa peptide of IFNβ. The subject peptides have been shown to effectincreased resistance to viral infection. Peptides of the invention canbe used to treat or prevent viral infections, to treat oncologicaldisorders, and to treat autoimmune disorders, such as multiplesclerosis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1C. Activated JAKs and receptor subunits are present in thenucleus of cells treated with type I IFNs. WISH cells were incubatedwith or without 1,000 U/ml of IFNα2 (FIG. 1A) or IFN (FIG. 1B) for theindicated times and their nuclei were purified and solubilized (seeMATERIALS and METHODS). Nuclear and cytoplasmic samples were subjectedto Western blotting against indicated antibodies. (FIG. 1C) WISH cellswere similarly treated with IFNτ and the nuclear fraction was Westernblotted with antibodies to IFNAR2 and IFNAR1.-tubulin (cytoplasm) and-lamin (nucleus) blots were performed to confirm the purity of nuclearfraction.

FIGS. 2A-2C. Nuclear translocation of IFNτ, IFNAR1, and IFNAR2 asdetermined by confocal microscopy. GFP fusion constructs of IFNτ,IFNAR1, and IFNAR2 were used to separately transfect WISH cells (seeMATERIALS and METHODS). IFNτ-GFP transfected cells measured nucleartranslocation of IFNτ (FIG. 2A). In the case of IFNAR1-GFP (FIG. 2B) andIFNAR2-GFP (FIG. 2C), cells were treated with 1,000 U/ml of IFNτ andreceptors were found to translocate to nuclei as seen by confocalmicroscopy.

FIG. 3. Type I IFN stimulation induces the association of IFNAR1, TYK2,STAT1α, and H3pY41 with the ISRE at the OAS1 promoter by ChIP assay.WISH cells were treated with 1,000 U/ml of IFNτ for 1 hr, then treatedwith 1% formaldehyde for 10 min. Details of ChIP assay are in MATERIALSand METHODS and described previously (Noon-Song et al., 2011). Abbrev:AR1, IFNAR1; pYH3, phosphorylated tyrosine 41 on histone H3.

FIG. 4. Association of TYK2, pSTAT1α, and H3pY41 with IFNAR1 in thenucleus of cells treated with a type I IFN. WISH cells were treated with1,000 U/ml of IFNα2 for 1 hr, after which a solubilized extract from theisolated nuclei was immunoprecipitated with antibodies to IFNAR1 andWestern blotted with the indicated antibodies (see MATERIALS andMETHODS).

FIGS. 5A-5B. Type I IFN treatment induces histone H3K9demethylation/acetylation as well as H3Y41 phosphorylation at the ISREof the promoter region of the OAS1 gene. (FIG. 5A) WISH cells weretreated with 1,000 U/ml of IFNτ for the indicated time and ChIP assayswere performed as in FIG. 3 using antibodies to H3K9ac, H3K9me3, andH3pY41. (FIG. 5B) Western blot for H3pY41 in WISH cells treated withIFNτ as indicated in FIG. 5A. Abbrev: H3K9ac, acetylated lysine 9 inhistone H3; H3pY41, phosphorylated tyrosine 41 in histone H3; H3K9me3,trimethylated lysine 9 in histone H3.

FIGS. 6A-6C. N-terminal truncated IFNα1(69-189)R9 or IFNβ(100-187)R9possessed antiviral activity and IFNα1(69-189)R9 protected againstrelapsing/remitting EAE in SJL/J mice. IFNα1(69-189)R9 (FIG. 6A), orIFNβ(100-187)R9 (FIG. 6B), or the control peptides without the R9 plasmamembrane penetration sequence were added to L929 cells (40,000 per well)and treated for 4 hr. Cells were infected with EMC virus (moi=0.01) for24 hr, followed by staining with crystal violet. (FIG. 6C) SJL/J mice(n=5), were injected i.p. with PBS (), IFNα mimetic, IFNα1(69-189)R9(▴, 15 μg/mouse), or the control peptide, IFNα1(69-189) (□, 15μg/mouse), every other day starting from day 12 post-immunization withMBP. Mice were followed daily. The mean daily severity of disease wasgraded as follows. 0, normal; 1, loss of tail tone; 2, hind legweakness; 3, paraparesis; 4, paraplegia; 5, moribund; and 6, death.

FIG. 7. Weight loss comparison. Mice (C57BL/6, n=3) were injected i.p.with IFNβ (Δ, 10³ U/mouse), IFNβ(100-179)R9(◯), 2×10³ U (200 μg), or2×10³ U (200 μg) of IFNα(69-189)R9 (□), i.p. on alternate days. Activityrefers to the antiviral activity assessed by cytopathic effect of EMCVon L cells. Body weight was measured daily. The average body weight ispresented as a percentage of initial weight, and the standard deviationis shown. The weight loss seen in IFNβ treated mice is not seen withIFNβ mimetic. On day 11, the difference between the IFNβ or IFNβ mimeticshowed a n<0.05.

FIG. 8. Lack of apoptosis in type I IFN mimetics in comparison withintact IFNα2. WISH cells (150,000) were seeded in a 6 well plate andgrown overnight. They were treated with type I IFN mimetics (100 U/ml),or IFNα2 (100 U/ml) for 4 days. Cells were doubly stained with Annexin Vand propidium iodide (PI) and analyzed by flow cytometry to measure theextent of apoptosis. The data shown indicate the percentage of apoptosisbased on cells staining for both Annexin V and PI from the analysis of10,000 cells.

FIG. 9. Type I IFN mimetics protect cells from VSV infection. MurineL929 cells were seeded in a microtiter plate and incubated withlipo-IFNα1(152-189), lipo-IFNβ(150-187), lipo-IFNτ(151-195), scrambledpeptide, or IFNα1 at the concentrations indicated for 2 hr. Cells werethen infected with 0.1 m.o.i. of VSV for 24 hr, stained with crystalviolet and the absorbance read.

FIG. 10. Type I IFN mimetics protect against EMC virus infection. HumanWISH cells (40,000 per well) were seeded in a microtiter plate and grownovernight. Treatment with IFNα and IFNβ mimetic peptides, or a controlscrambled peptide was for 4 hr. Cells were infected with EMC virus (0.01moi) for 24 hr, followed by staining with crystal violet.

FIG. 11. Inhibition of vaccinia virus replication by type I IFNmimetics. BSC40 cells were grown to confluence and treated with theC-terminal peptides of IFNs α, β, and τ for 2 hr. Lipo- refers to theconjugated palmitic acid added for allowing these peptides to gain entryacross plasma membrane. Cells were then infected with 0.01 m.o.i. ofvaccinia virus for 1 hr, followed by washing and addition of freshmedium. Forty eight hours later, cells were stained with crystal violetand plaques counted. A scrambled peptide is used as a negative control.Intact IFNα1 added at 2000 U/ml did not protect against VV infection.

FIG. 12. Lipo-IFNα1(152-189) protects mice against vaccinia virus, whileintact IFN does not. Mice (C57BL/6, n=5) were infected i.n. with 2×10⁶pfu of vaccinia virus. Starting on day 0, PBS, lipo-IFNα1(152-189) (200μg), scrambled peptide (200 μg), or murine IFNα1 (2,000 U) wereadministered i.p. in a volume of 100 μl for six consecutive days.Survival of mice was followed.

FIG. 13. Type I IFN mimetic do not show weight loss in comparison tointact IFN. Mice (C57BL/6, n=3) were injected i.p. with murine IFNα1 (Δ,5×10³ U/mouse), Lipo-IFNα(152-189), 5×10³ U (100 μg, ▪), or PBS (◯),i.p. on alternate days. Activity refers to the antiviral activityassessed by cytopathic effect of EMCV on L cells. Body weight wasmeasured daily. The average body weight is presented as a percentage ofinitial weight, and the standard deviation is shown. The weight lossseen in IFNα treated mice is not seen with IFNα mimetic. On day 11, thedifference between the IFNα and IFNα mimetic showed a p<0.05.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NO:1 is a peptide mimetic of human IFNα1.

SEQ ID NO:2 is a peptide mimetic of human IFNβ1.

SEQ ID NO:3 is a peptide mimetic of SEQ ID NO:1 that further comprises alipophilic sequence on the N-terminus of the peptide.

SEQ ID NO:4 is a peptide mimetic of SEQ ID NO:2 that further comprises alipophilic sequence on the N-terminus of the peptide.

SEQ ID NO:5 is a peptide mimetic of human IFNα2.

SEQ ID NO:6 is a peptide mimetic of human IFNα4.

SEQ ID NO:7 is the amino acid sequence of a peptide designated herein asMuIFNγ(95-132).

SEQ ID NO:8 is the amino acid sequence of a peptide designated herein ashuIFNγ(95-134).

SEQ ID NO:9 is the amino acid sequence of a peptide designated herein asTkip.

SEQ ID NO:10 is the amino acid sequence of a peptide designated hereinas SOCS1-KIR.

SEQ ID NO:11 is the full-length precursor human IFNα1 amino acidsequence.

SEQ ID NO:12 is the full-length precursor human IFNβ1 amino acidsequence.

SEQ ID NO:13 is a histone H3 peptide.

SEQ ID NO:14 is a primer for amplifying human OAS1 promoter region.

SEQ ID NO:15 is a primer for amplifying human OAS1 promoter region.

SEQ ID NO:16 is a primer for amplifying human β-actin promoter region.

SEQ ID NO:17 is a primer for amplifying human β-actin promoter region.

SEQ ID NO:18 is a nuclear localization sequence of IFNAR2.

SEQ ID NOs:19-37 are cell-penetrating peptides that can be used inaccordance with the subject invention.

SEQ ID NO:38 is a peptide mimetic of human lipo-IFNα1.

SEQ ID NO:39 is a peptide mimetic of human IFNβ.

SEQ ID NO:40 is a peptide mimetic of ovine lipo-IFNτ.

SEQ ID NO:41 is a peptide having a scrambled sequence of the lipo-IFNτpeptide.

SEQ ID NO:42 is the full-length ovine IFN-tau amino acid sequence.

DETAILED DESCRIPTION OF THE INVENTION

The subject invention pertains to agonist peptides of type I interferonsand methods of using the peptides. These peptides are based on the aminoacid sequence of the C-terminus region of the type I IFN molecules andare capable of binding to the cytoplasmic domain of type I IFN receptorsand activating the receptor. Surprisingly, these peptides were found topossess the same or similar biological activity as that associated withthe full-length, mature type I IFN proteins, even though these peptidesdo not bind to the extracellular domain of the type I IFN receptors. Inone embodiment, the peptide is a peptide of IFNα protein (e.g., a humanIFNα protein). In another embodiment, the peptide is a peptide of IFNβprotein (e.g., a human IFNβ protein). In a still further embodiment, thepeptide is a peptide of an IFN-tau (IFNτ) protein. The subject peptideshave been shown to provide for increased resistance to viral infectionin cells and in animals. Peptides of the invention can be used to treator prevent viral infections, to treat oncological disorders, and totreat autoimmune disorders, such as multiple sclerosis. Peptides of theinvention generally lack the side effects associated with use offull-length type I IFNs.

In an exemplified embodiment, the huIFNα1 (69-189) peptide (SEQ ID NO:1)based on human IFNα1 has an amino acid sequence corresponding to aminoacid residues 69 through 189 of the full-length human IFNα 1 protein(SEQ ID NO:11), or a fragment or variant thereof that retainssubstantially the same activity as the full-length non-variant peptide.In another embodiment, the huIFNα1 (152-189) peptide (SEQ ID NO:38) hasan amino acid sequence corresponding to amino acid residues 152 through189 of the full-length human IFNα1 protein, or a fragment or variantthereof that retains substantially the same activity as the full-lengthnon-variant peptide. In a further embodiment, the huIFNβ1 (100-187)peptide (SEQ ID NO:2) based on human IFNβ1 has an amino acid sequencecorresponding to amino acid residues 100 through 187 of the full-lengthhuman IFNβ1 protein (SEQ ID NO:12), or a fragment or variant thereofthat retains substantially the same activity as the full-lengthnon-variant peptide. In another embodiment, the huIFNβ1 (150-187)peptide (SEQ ID NO:39) has an amino acid sequence corresponding to aminoacid residues 150 through 187 of the full-length human IFNβ1 protein, ora fragment or variant thereof that retains substantially the sameactivity as the full-length non-variant peptide. In another embodiment,the ovine IFNτ (156-195) peptide (SEQ ID NO:40) has an amino acidsequence corresponding to amino acid residues 156 through 195 of thefull-length ovine IFNτ protein, or a fragment or variant thereof thatretains substantially the same activity as the full-length non-variantpeptide. In another embodiment, a peptide of the invention has the aminoacid sequence shown in SEQ ID NO:5 or SEQ ID NO:6, or a fragment orvariant thereof that retains substantially the same activity as thefull-length non-variant peptide. Peptides of the invention can beprovided in purified or isolated form.

In one embodiment, a peptide of the invention comprises a lipophilicsequence or moiety that facilitates penetration through a cell membranefor entry into a cell. In one embodiment, a peptide of the inventioncomprises one or more arginine or lysine amino acids at one or bothtermini of the peptide. In a specific embodiment, a peptide of theinvention comprises one or more arginine amino acids at the N-terminusof the peptide. For example, a peptide can comprise 1, 2, 3, 4, 5, 6, 7,8, 9, 10, or more arginine and/or lysine amino acids at one or bothtermini. In an exemplified embodiment, a peptide of the invention hasthe amino acid sequence shown in SEQ ID NO:3 or SEQ ID NO:4. In anotherembodiment, a peptide of the invention comprises a fatty acid moiety,e.g., a carboxylic acid with a long aliphatic tail, attached to thepeptide. Examples of fatty acids contemplated within the scope of theinvention include, but are not limited to, caprylic acid, capric acid,lauric acid, myristic acid, palmitic acid, stearic acid, arachidic acid,behenic acid, lignoceric acid, and cerotic acid. In a specificembodiment, a peptide of the invention comprises a palmitate or palmiticacid (hexadecanoic acid) attached to the peptide, typically at the N-and/or C-terminus of the peptide. In a further embodiment, a peptide ofthe invention comprises a nuclear localization sequence (NLS).

The discovery of peptide agonists of type I interferons is highlyunexpected. Use of synthetic peptide agonists rather than thefull-length type I IFN molecules offers advantages such as targeting ofspecific cells and immune system components. Also, specific amino acidresidues of the peptides can be easily and rapidly modified to allow forgeneration of more effective agonists or antagonists.

As those skilled in the art can readily appreciate, there can be anumber of variant sequences of a protein found in nature, in addition tothose variants that can be artificially created by the skilled artisanin the lab. The peptides of the subject invention encompasses thosespecifically exemplified herein, as well as any natural variantsthereof, as well as any variants which can be created artificially, solong as those variants retain the desired biological activity.

The peptides contemplated in the subject invention include the specificpeptides exemplified herein as well as equivalent peptides which may be,for example, somewhat longer or shorter than the peptides exemplifiedherein. For example, using the teachings provided herein, a personskilled in the art could readily make peptides having from 1 to about 5,10, 15, 20, 25, 30, 35, 40, 50, 60, 70 or more amino acids added to, orremoved from, either end of the disclosed peptides using standardtechniques known in the art. In one embodiment, amino acids are removedfrom the N-terminus of a peptide of the invention. In a specificembodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 50, 60, 70 or more amino acids can, independently,be removed from either or both ends of a peptide of the invention.Preferably, any added amino acids would be the same as the correspondingamino acids of a mature full-length type I IFN protein. The skilledartisan, having the benefit of the teachings disclosed in the subjectapplication, could easily determine whether a variant peptide retainedthe biological activity of the specific peptides exemplified herein.Such a longer or shorter peptide would be within the scope of thesubject invention as long as said peptide does not encompass the entirefull-length IFN protein and said longer or shorter peptide retainssubstantially the same relevant biological activity as the peptidesexemplified herein. For example, a longer or shorter variant of thehuIFNα 1 (69-189) (SEQ ID NO:1) peptide would fall within the scope ofthe subject invention if the variant peptide had the ability to increasecellular resistance to viral infection.

Also within the scope of the subject invention are peptides which havethe same amino acid sequences of a peptide exemplified herein except foramino acid substitutions, additions, or deletions within the sequence ofthe peptide, as long as these variant peptides retain substantially thesame relevant biological activity as the peptides specificallyexemplified herein. For example, conservative amino acid substitutionswithin a peptide which do not affect the ability of the peptide to, forexample, to increase cellular resistance to viral infection would bewithin the scope of the subject invention. Thus, the peptides disclosedherein should be understood to include variants and fragments, asdiscussed above, of the specifically exemplified sequences.

The subject invention further includes nucleotide sequences which encodethe peptides disclosed herein. These nucleotide sequences can be readilyconstructed by those skilled in the art having the knowledge of theprotein and peptide amino acid sequences which are presented herein. Aswould be appreciated by one skilled in the art, the degeneracy of thegenetic code enables the artisan to construct a variety of nucleotidesequences that encode a particular peptide or protein. The choice of aparticular nucleotide sequence could depend, for example, upon the codonusage of a particular expression system.

The subject invention contemplates the use of the peptides describedherein in pharmaceutical compositions for administration to an animal orhuman for the treatment of clinically important disease conditions thatare amenable to treatment with a full-length interferon. For example,using the teachings described herein, the skilled artisan can use thesubject invention to modulate or stimulate the immune response of ananimal or human. Similarly, the subject peptides can be used to treatcertain viral infections, as well as to treat certain forms of cancer ortumors. The peptides of the subject invention can be prepared inpharmaceutically acceptable carriers or diluents for administration tohumans or animals in a physiologically tolerable form. Materials andmethods for preparing such compositions are known in the art.

The peptides of the subject invention can be administered using avariety of techniques that are known in the art. The peptides can beencapsulated in liposomes that are targeted to specific cells or tissuesand the liposome-encapsulated peptides delivered to the cells or tissueeither in vitro, in vivo, or ex vivo. Procedures for preparing liposomesand encapsulating compounds within the liposome are well known in theart. See, for example, U.S. Pat. No. 5,252,348, which issued to Schreieret al. Peptides can also be conjugated or attached to other molecules,such as an antibody, that targeted a specific cell or tissue. Peptidescan also be administered using a drug delivery system similar to thatdescribed in U.S. Pat. No. 4,625,014, which issued to Senter et al.

As described herein, the peptide sequences of the subject invention canalso be the basis for producing peptides that act as type I IFNantagonists. These antagonists are also within the scope of the subjectinvention. Inhibition or antagonism of interferon function withoutagonist activity can be accomplished through the use of anti-peptideantibodies or modification of residues within the peptide itself. Anespecially productive means for generation of peptide antagonists hasbeen substitution of L-amino acids with D-amino acids. The efficacy ofthis approach has been well characterized in the generation of argininevasopressin analogs with selectively enhanced antidiuretic antagonism byappropriate substitution of L-amino acids with D-amino acids (Manning etal., 1985). Further, not only can antagonism be produced with D-aminoacid substitutions, but this antagonism can be directed toward aspecific function. Production of potent antagonist peptides can be ofvalue in specifically manipulating immune function.

A further aspect of the claimed invention is the use of the claimedpeptides to produce antibodies, both polyclonal and monoclonal. Theseantibodies can be produced using standard procedures well known to thoseskilled in the art. These antibodies may be used as diagnostic andtherapeutic reagents. For example, antibodies that bind to the humanIFNα1(69-189) (SEQ ID NO:1) or IFNα1(152-189) (SEQ ID NO:38) peptide canbe used as an antagonist to block the function of IFNα. Similarly,antibodies that bind to human IFNβ1(100-187) (SEQ ID NO:2) orIFNβ1(150-187) (SEQ ID NO:39) peptide can be used as an antagonist toblock the function of IFNβ. Antibodies that bind to ovine IFNτ(156-195)(SEQ ID NO:40) peptide can be used as an antagonist to block thefunction of IFNτ. Antibodies that are reactive with the peptides of thesubject invention can also be used to purify type I IFN protein orpeptides from a crude mixture. In one embodiment, an antibody bindsspecifically to the human IFNα1(69-189) (SEQ ID NO:1) or IFNα1(152-189)(SEQ ID NO:38) peptide. In another embodiment, an antibody bindsspecifically to the human IFNβ1(100-187) (SEQ ID NO:2) or IFNβ1(150-187)(SEQ ID NO:39) peptide.

An antibody that is contemplated by the present invention can be in anyof a variety of forms, including a whole immunoglobulin, an antibodyfragment such as Fv, Fab, and similar fragments, as well as a singlechain antibody that includes the variable domain complementaritydetermining regions (CDR), and similar forms, all of which fall underthe broad term “antibody,” as used herein.

The term “antibody fragment” refers to a portion of a full-lengthantibody, generally the antigen binding or variable region. Examples ofantibody fragments include Fab, Fab′, F(ab′)₂ and Fv fragments. Papaindigestion of antibodies produces two identical antigen bindingfragments, called the Fab fragment, each with a single antigen bindingsite, and a residual “Fc” fragment, so-called for its ability tocrystallize readily. Pepsin treatment of an antibody yields an F(ab′)₂fragment that has two antigen binding fragments, which are capable ofcross-linking antigen, and a residual other fragment (which is termedpFc′). Additional fragments can include diabodies, linear antibodies,single-chain antibody molecules, and multispecific antibodies formedfrom antibody fragments. As used herein, “antigen binding fragment” withrespect to antibodies, refers to, for example, Fv, F(ab) and F(ab′)₂fragments.

Antibody fragments can retain an ability to selectively bind with theantigen or analyte are contemplated within the scope of the inventionand include:

(1) Fab is the fragment of an antibody that contains a monovalentantigen-binding fragment of an antibody molecule. A Fab fragment can beproduced by digestion of whole antibody with the enzyme papain to yieldan intact light chain and a portion of one heavy chain.

(2) Fab′ is the fragment of an antibody molecule can be obtained bytreating whole antibody with pepsin, followed by reduction, to yield anintact light chain and a portion of the heavy chain. Two Fab′ fragmentsare obtained per antibody molecule. Fab′ fragments differ from Fabfragments by the addition of a few residues at the carboxyl terminus ofthe heavy chain CH1 domain including one or more cysteines from theantibody hinge region.

(3) (Fab′)₂ is the fragment of an antibody that can be obtained bytreating whole antibody with the enzyme pepsin without subsequentreduction. F(ab′)₂ is a dimer of two Fab′ fragments held together by twodisulfide bonds.

(4) Fv is the minimum antibody fragment that contains a complete antigenrecognition and binding site. This region consists of a dimer of oneheavy and one light chain variable domain in a tight, non-covalentassociation (V_(H)-V_(L) dimer). It is in this configuration that thethree CDRs of each variable domain interact to define an antigen-bindingsite on the surface of the V_(H)-V_(L) dimer. Collectively, the six CDRsconfer antigen-binding specificity to the antibody. However, even asingle variable domain (or half of an Fv comprising only three CDRsspecific for an antigen) has the ability to recognize and bind antigen,although at a lower affinity than the entire binding site.

(5) Single chain antibody (“SCA”), defined as a genetically engineeredmolecule containing the variable region of the light chain (V_(L)), thevariable region of the heavy chain (V_(H)), linked by a suitablepolypeptide linker as a genetically fused single chain molecule. Suchsingle chain antibodies are also referred to as “single-chain Fv” or“sFv” antibody fragments. Generally, the Fv polypeptide furthercomprises a polypeptide linker between the V_(H) and V_(L) domains thatenables the sFv to form the desired structure for antigen binding. For areview of sFv fragments, see Pluckthun in The Pharmacology of MonoclonalAntibodies, vol. 113, Rosenburg and Moore eds. Springer-Verlag, N.Y.,pp. 269 315 (1994).

Antibodies within the scope of the invention can be of any isotype,including IgG, IgA, IgE, IgD, and IgM. IgG isotype antibodies can befurther subdivided into IgG1, IgG2, IgG3, and IgG4 subtypes. IgAantibodies can be further subdivided into IgA1 and IgA2 subtypes.

Antibodies of the subject invention can be genus or species specific toa target. Antibodies of the invention can be prepared using standardtechniques known in the art. Antibodies useful in the invention can bepolyclonal or monoclonal antibodies. Monoclonal antibodies can beprepared using standard methods known in the art (Kohler et al., 1975).Antibodies of the invention can be mammalian antibodies, includingmouse, rat, goat, rabbit, pig, dog, cat, monkey, chimpanzee, ape, orhuman.

The subject peptides can also be used in the design of new drugs thatbind to the cytoplasmic domain of a type I IFN receptor. Knowledge ofpeptide sequences that induce type I IFN biological activity uponbinding of the peptide to a localized region on the type I IFN receptorenables a skilled artisan to develop additional bioactive compoundsusing rational drug design techniques. Thus, the skilled artisan canprepare both agonist and antagonist drugs using the teachings describedherein.

The subject invention also concerns compositions comprising one or morepeptides or polynucleotides of the invention. In one embodiment, acomposition further comprises a suitable carrier, diluent, or buffer.Compositions contemplated within the scope of the invention can compriseone or more peptides or polynucleotides of the invention and,optionally, one or more other antiviral compounds. For example, apeptide of the invention can be provided in a composition with one ormore of IFNα, IFNβ, IFNγ, acyclovir (Zovirax), zidovudine (AZT),lamivudine (3TC), zanamivir (Relenza), oseltamivir (Tamiflu),valacyclovir (Valtrex), amantadine (Symmetrel), rimantadine (Flumadine),cidofovir (Vistide), foscarnet (Foscavir), ganciclovir (Cytovene),ribavirin (Virazole), nelfinavir (Viracept), ritonavir (Norvir),rifampin (Rifadin), and famciclovir (Famvir). In one embodiment, thecomposition comprises a peptide or polynucleotide of the invention in apharmaceutically or physiologically acceptable carrier, buffer, ordiluent. Compositions of the invention can comprise additional peptidessuch as an IFNγ mimetic. Examples of IFNγ mimetic peptides are describedin U.S. Pat. Nos. 5,770,191 and 6,120,762. In one embodiment, the IFNγmimetic peptide comprises the amino acid sequence shown in SEQ ID NO:7(MuIFNγ(95-132)) or SEQ ID NO:8 (huIFNγ(95-134)), or a fragment orvariant thereof that exhibits antiviral activity. In one embodiment, acomposition of the invention can comprise one or more peptidescomprising the amino acid sequence shown in SEQ ID NO:9 (Tkip peptide),or a fragment or variant thereof that exhibits antiviral activity,and/or a peptide comprising the amino acid sequence shown in SEQ IDNO:10 (SOCS1-KIR), or a fragment or variant thereof that exhibitsantiviral activity.

The methods of the invention contemplate that a peptide, polynucleotide,composition, or other agent of the invention is administered to theperson or animal prior to infection by a virus. Also contemplated withinthe scope of the methods is that a peptide, polynucleotide, composition,or other agent of the invention is administered at the time of infectionor after the person or animal has been infected. In one embodiment, aperson or animal to be treated is one that has previously beenvaccinated against infection by a virus, such as a poxvirus. In anotherembodiment, the person or animal has not been previously vaccinatedagainst the virus.

In one embodiment, peptides, polynucleotides, antibodies, and otheragents of the invention are modified so as to enhance uptake into acell. In one embodiment, a lipophilic group is attached to a peptide,polynucleotide, or other agent of the invention. In one embodiment, apalmitic acid is attached to a peptide of the invention. In a specificembodiment, a palmitoyl-lysine group is attached to the peptide, forexample at the N-terminus of the peptide. Other methods for enhancinguptake of a peptide, polynucleotide, and antibody into a cell are knownin the art and are contemplated within the scope of the invention.

Peptides, polynucleotides, antibodies, compositions, and other agents ofthe invention can also be delivered into cells by encapsulation of thepeptide, polynucleotide, antibody, and other agents of the inventionwithin a liposome. Methods for encapsulation of peptides,polynucleotides, antibodies, and other agents of the invention withinliposomes are well known in the art.

Peptides having substitution of amino acids other than thosespecifically exemplified in the subject peptides are also contemplatedwithin the scope of the present invention. For example, non-naturalamino acids can be substituted for the amino acids of a peptide of theinvention, so long as the peptide having substituted amino acids retainssubstantially the same activity as the peptide in which amino acids havenot been substituted. Examples of non-natural amino acids include, butare not limited to, ornithine, citrulline, hydroxyproline, homoserine,phenylglycine, taurine, iodotyrosine, 2,4-diaminobutyric acid, α-aminoisobutyric acid, 4-aminobutyric acid, 2-amino butyric acid, γ-aminobutyric acid, ε-amino hexanoic acid, 6-amino hexanoic acid, 2-aminoisobutyric acid, 3-amino propionic acid, norleucine, norvaline,sarcosine, homocitrulline, cysteic acid, τ-butylglycine, τ-butylalanine,phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids,designer amino acids such as β-methyl amino acids, C-methyl amino acids,N-methyl amino acids, and amino acid analogues in general. Non-naturalamino acids also include amino acids having derivatized side groups.Furthermore, any of the amino acids in the protein can be of the D(dextrorotary) form or L (levorotary) form.

Amino acids can be generally categorized in the following classes:non-polar, uncharged polar, basic, and acidic. Conservativesubstitutions whereby a peptide having an amino acid of one class isreplaced with another amino acid of the same class fall within the scopeof the subject invention so long as the peptide having the substitutionstill retains substantially the same biological activity as a peptidethat does not have the substitution. Table 1 below provides a listing ofexamples of amino acids belonging to each class.

TABLE 1 Class of Amino Acid Examples of Amino Acids Nonpolar Ala, Val,Leu, Ile, Pro, Met, Phe, Trp Uncharged Polar Gly, Ser, Thr, Cys, Tyr,Asn, Gln Acidic Asp, Glu Basic Lys, Arg, His

Single letter amino acid abbreviations are defined in Table 2.

TABLE 2 Letter Symbol Amino Acid A Alanine B Asparagine or aspartic acidC Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine HHistidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine PProline Q Glutamine R Arginine S Serine T Threonine V Valine WTryptophan Y Tyrosine Z Glutamine or glutamic acid

The peptides of the present invention can be formulated intopharmaceutically-acceptable salt forms. Pharmaceutically-acceptable saltforms include the acid addition salts and include hydrochloric,hydrobromic, nitric, phosphoric, carbonic, sulphuric, and organic acidslike acetic, propionic, benzoic, succinic, fumaric, mandelic, oxalic,citric, tartaric, maleic, and the like. Pharmaceutically-acceptable baseaddition salts include sodium, potassium, calcium, ammonium, andmagnesium salts. Pharmaceutically-acceptable salts of the peptides ofthe invention can be prepared using conventional techniques.

The subject invention also concerns polynucleotide expression constructsthat comprise a polynucleotide of the present invention comprising anucleotide sequence encoding a peptide of the present invention. In oneembodiment, the polynucleotide encodes a peptide comprising the aminoacid sequence shown in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ IDNO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ ID NO:39, or SEQ IDNO:40, or a fragment or variant thereof that exhibits substantially thesame activity as the full-length non-variant peptide.

As used herein, the term “expression construct” refers to a combinationof nucleic acid sequences that provides for transcription of an operablylinked nucleic acid sequence. As used herein, the term “operably linked”refers to a juxtaposition of the components described wherein thecomponents are in a relationship that permits them to function in theirintended manner. In general, operably linked components are incontiguous relation.

Expression constructs of the invention will also generally includeregulatory elements that are functional in the intended host cell inwhich the expression construct is to be expressed. Thus, a person ofordinary skill in the art can select regulatory elements for use in, forexample, bacterial host cells, yeast host cells, plant host cells,insect host cells, mammalian host cells, and human host cells.Regulatory elements include promoters, transcription terminationsequences, translation termination sequences, enhancers, andpolyadenylation elements.

An expression construct of the invention can comprise a promotersequence operably linked to a polynucleotide sequence encoding a peptideof the invention. Promoters can be incorporated into a polynucleotideusing standard techniques known in the art. Multiple copies of promotersor multiple promoters can be used in an expression construct of theinvention. In a preferred embodiment, a promoter can be positioned aboutthe same distance from the transcription start site as it is from thetranscription start site in its natural genetic environment. Somevariation in this distance is permitted without substantial decrease inpromoter activity. A transcription start site is typically included inthe expression construct.

For expression in animal cells, an expression construct of the inventioncan comprise suitable promoters that can drive transcription of thepolynucleotide sequence. If the cells are mammalian cells, thenpromoters such as, for example, actin promoter, metallothioneinpromoter, NF-kappaB promoter, EGR promoter, SRE promoter, IL-2 promoter,NFAT promoter, osteocalcin promoter, SV40 early promoter and SV40 latepromoter, Lck promoter, BMP5 promoter, TRP-1 promoter, murine mammarytumor virus long terminal repeat promoter, STAT promoter, or animmunoglobulin promoter can be used in the expression construct. Thebaculovirus polyhedrin promoter can be used with an expression constructof the invention for expression in insect cells. Promoters suitable foruse with an expression construct of the invention in yeast cellsinclude, but are not limited to, 3-phosphoglycerate kinase promoter,glyceraldehyde-3-phosphate dehydrogenase promoter, metallothioneinpromoter, alcohol dehydrogenase-2 promoter, and hexokinase promoter.

For expression in prokaryotic systems, an expression construct of theinvention can comprise promoters such as, for example, alkalinephosphatase promoter, tryptophan (trp) promoter, lambda P_(L) promoter,β-lactamase promoter, lactose promoter, phoA promoter, T3 promoter, T7promoter, or tac promoter (de Boer et al., 1983).

If the expression construct is to be provided in a plant cell, plantviral promoters, such as, for example, the cauliflower mosaic virus(CaMV) 35S (including the enhanced CaMV 35S promoter (see, for exampleU.S. Pat. No. 5,106,739)) or 19S promoter can be used. Plant promoterssuch as prolifera promoter, Ap3 promoter, heat shock promoters, T-DNA1′- or 2′-promoter of A. tumafaciens, polygalacturonase promoter,chalcone synthase A (CHS-A) promoter from petunia, tobacco PR-1apromoter, ubiquitin promoter, actin promoter, alcA gene promoter, pin2promoter (Xu et al., 1993), maize WipI promoter, maize trpA genepromoter (U.S. Pat. No. 5,625,136), maize CDPK gene promoter, andRUBISCO SSU promoter (U.S. Pat. No. 5,034,322) can also be used.Seed-specific promoters such as the promoter from a β-phaseolin gene (ofkidney bean) or a glycinin gene (of soybean), and others, can also beused. Constitutive promoters (such as the CaMV, ubiquitin, actin, or NOSpromoter), tissue-specific promoters (such as the E8 promoter fromtomato), developmentally-regulated promoters, and inducible promoters(such as those promoters than can be induced by heat, light, hormones,or chemicals) are contemplated for use with the polynucleotides of theinvention.

Expression constructs of the invention may optionally contain atranscription termination sequence, a translation termination sequence,signal peptide sequence, and/or enhancer elements. Transcriptiontermination regions can typically be obtained from the 3′ untranslatedregion of a eukaryotic or viral gene sequence. Transcription terminationsequences can be positioned downstream of a coding sequence to providefor efficient termination. Signal peptides are a group of short aminoterminal sequences that encode information responsible for therelocation of an operably linked peptide to a wide range ofpost-translational cellular destinations, ranging from a specificorganelle compartment to sites of protein action and the extracellularenvironment. Targeting a peptide to an intended cellular and/orextracellular destination through the use of operably linked signalpeptide sequence is contemplated for use with the peptides of theinvention. Chemical enhancers are cis-acting elements that increase genetranscription and can also be included in the expression construct.Chemical enhancer elements are known in the art, and include, but arenot limited to, the CaMV 35S enhancer element, cytomegalovirus (CMV)early promoter enhancer element, and the SV40 enhancer element. DNAsequences which direct polyadenylation of the mRNA encoded by thestructural gene can also be included in the expression construct.

Unique restriction enzyme sites can be included at the 5′ and 3′ ends ofthe expression construct to allow for insertion into a polynucleotidevector. As used herein, the term “vector” refers to any genetic element,including for example, plasmids, cosmids, chromosomes, phage, virus, andthe like, which is capable of replication when associated with propercontrol elements and which can transfer polynucleotide sequences betweencells. Vectors contain a nucleotide sequence that permits the vector toreplicate in a selected host cell. A number of vectors are available forexpression and/or cloning, and include, but are not limited to, pBR322,pUC series, M13 series, and pBLUESCRIPT vectors (Stratagene, La Jolla,Calif.).

Polynucleotides, vectors, and expression constructs of the subjectinvention can be introduced into a cell by methods known in the art.Such methods include transfection, microinjection, electroporation,lipofection, cell fusion, calcium phosphate precipitation, and bybiolistic methods. In one embodiment, a polynucleotide or expressionconstruct of the invention can be introduced in vivo via a viral vectorsuch as adeno-associated virus (AAV), herpes simplex virus (HSV),papillomavirus, adenovirus, and Epstein-Barr virus (EBV). Attenuated ordefective forms of viral vectors that can be used with the subjectinvention are known in the art. Typically, defective virus is notcapable of infection after the virus is introduced into a cell.Polynucleotides, vectors, and expression constructs of the invention canalso be introduced in vivo via lipofection (DNA transfection vialiposomes prepared from synthetic cationic lipids) (Felgner et al.,1987). Synthetic cationic lipids (LIPOFECTIN, Invitrogen Corp., LaJolla, Calif.) can be used to prepare liposomes to encapsulate apolynucleotide, vector, or expression construct of the invention. Apolynucleotide, vector, or expression construct of the invention canalso be introduced in vivo as naked DNA using methods known in the art,such as transfection, microinjection, electroporation, calcium phosphateprecipitation, and by biolistic methods.

Polynucleotides and peptides of the subject invention can also bedefined in terms of more particular identity and/or similarity rangeswith those exemplified herein. The sequence identity will typically begreater than 60%, preferably greater than 75%, more preferably greaterthan 80%, even more preferably greater than 90%, and can be greater than95%. The identity and/or similarity of a sequence can be 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% as compared to a sequenceexemplified herein. Unless otherwise specified, as used herein percentsequence identity and/or similarity of two sequences can be determinedusing the algorithm of Karlin and Altschul (1990), modified as in Karlinand Altschul (1993). Such an algorithm is incorporated into the NBLASTand XBLAST programs of Altschul et al. (1990). BLAST searches can beperformed with the NBLAST program, score=100, wordlength=12, to obtainsequences with the desired percent sequence identity. To obtain gappedalignments for comparison purposes, Gapped BLAST can be used asdescribed in Altschul et al. (1997). When utilizing BLAST and GappedBLAST programs, the default parameters of the respective programs(NBLAST and XBLAST) can be used. See NCBI/NIH website.

The subject invention also contemplates those polynucleotide molecules(encoding peptides of the invention) having sequences which aresufficiently homologous with the polynucleotide sequences encoding apeptide of the invention so as to permit hybridization with thatsequence under standard stringent conditions and standard methods(Maniatis, T. et al., 1982). As used herein, “stringent” conditions forhybridization refers to conditions wherein hybridization is typicallycarried out overnight at 20-25 C below the melting temperature (Tm) ofthe DNA hybrid in 6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/mldenatured DNA. The melting temperature is described by the followingformula (Beltz, G. A. et al., 1983):

Tm=81.5C+16.6 Log [Na+]+0.41(%G+C)−0.61(% formamide)−600/length ofduplex in base pairs.

Washes are typically carried out as follows:

(1) Twice at room temperature for 15 minutes in 1×SSPE, 0.1% SDS (lowstringency wash).

(2) Once at Tm-20 C for 15 minutes in 0.2×SSPE, 0.1% SDS (moderatestringency wash).

As used herein, the terms “nucleic acid” and “polynucleotide sequence”refer to a deoxyribonucleotide or ribonucleotide polymer in eithersingle- or double-stranded form, and unless otherwise limited, wouldencompass known analogs of natural nucleotides that can function in asimilar manner as naturally-occurring nucleotides. The polynucleotidesequences include both the DNA strand sequence that is transcribed intoRNA and the RNA sequence that is translated into protein. Thepolynucleotide sequences include both full-length sequences as well asshorter sequences derived from the full-length sequences. It isunderstood that a particular polynucleotide sequence includes thedegenerate codons of the native sequence or sequences which may beintroduced to provide codon preference in a specific host cell. Thepolynucleotide sequences falling within the scope of the subjectinvention further include sequences which specifically hybridize withthe sequences coding for a peptide of the invention. The polynucleotideincludes both the sense and antisense strands as either individualstrands or in the duplex.

The subject invention also concerns methods for inducing an antiviralstate in a cell. In one embodiment, a cell is contacted with aneffective amount of a peptide, polynucleotide, or a composition of theinvention. In one embodiment, the cell is not infected with a virusprior to contact with a peptide, polynucleotide, or composition of theinvention. In another embodiment, the cell is already infected with avirus prior to contact with a peptide, polynucleotide, or composition ofthe invention. In one embodiment, the peptide has the amino acidsequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ IDNO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ ID NO:39, or SEQ ID NO:40, or afragment or variant thereof that exhibits antiviral activity. In oneembodiment, the composition comprises a peptide of the invention and anantiviral drug and/or a IFN mimetic. The cell can be a human ormammalian cell. In one embodiment, the cell can be a keratinocyte, afibroblast, a macrophage, or a lymphocyte. Peptides, polynucleotides,compositions, and/or other agents of the invention can be delivered to acell either through direct contact of peptide, etc. with the cell or viaa carrier means. Carrier means for delivering compositions to cells areknown in the art and include encapsulating the composition in a liposomemoiety, and attaching the peptide or polynucleotide to a protein ornucleic acid that is targeted for delivery to the target cell. PublishedU.S. Patent Application Nos. 20030032594 and 20020120100 disclose aminoacid sequences that can be coupled to another peptide, protein, ornucleic acid and that allows the peptide, protein, or nucleic acid to betranslocated across biological membranes. Published U.S. PatentApplication No. 20020035243 also describes compositions for transportingbiological moieties, such as peptides and proteins across cell membranesfor intracellular delivery. Peptides can also be delivered using apolynucleotide that encodes a subject peptide. In one embodiment, thepolynucleotide is delivered to the cell where it is taken up and thepolynucleotide is transcribed into RNA and the RNA is translated intothe encoded peptide. Antiviral activity can be induced in a cell againstviruses such as vaccinia virus, EMC virus, influenza virus, herpessimplex virus (e.g., HSV-1), cytomegalovirus, herpes zoster virus, andother herpes viruses, poxvirus, coxsackie virus, lentivirus (e.g., HIV),picornavirus and vesicular stomatitis virus (VSV). Methods of theinvention can be conducted in vitro or in vivo.

The subject invention also concerns methods for preventing or treating aviral infection and/or a viral associated disorder in a patient. In oneembodiment, the disorder is hepatitis (e.g., caused by hepatitis B orhepatitis C virus). In one embodiment, an effective amount of a peptide,polynucleotide, and/or composition of the present invention isadministered to a patient having a viral infection and who is in need oftreatment thereof. In another embodiment, the patient is not yetinfected with a virus or does not yet have a viral associated disorder.Optionally, the patient is a person or animal at risk of virus infectionor at risk of developing a viral associated disorder. In one embodiment,the peptide has the amino acid sequence in SEQ ID NO:1, SEQ ID NO:2, SEQID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ IDNO:39, or SEQ ID NO:40, or a fragment or variant thereof that exhibitsantiviral activity. Methods of the invention can also further compriseadministering one or more compounds useful for treating a viralinfection or viral associated disorder. Such compounds can beadministered prior to, in conjunction with, and/or subsequent toadministration of a peptide, polynucleotide, and/or composition of thepresent invention. The patient can be a human or other mammal, such as adog, cat, or horse, or other animals having the disorder. Means foradministering and formulating peptides and polynucleotides foradministration to a patient are known in the art, examples of which aredescribed herein. Peptides, polynucleotides, and/or compositions of theinvention can be delivered to a cell either through direct contact ofpeptide, polynucleotide, or composition with the cell or via a carriermeans. In one embodiment, a peptide, polynucleotide, or composition ofthe invention comprises an attached group that enhances cellular uptakeof the peptide. In one embodiment, the peptide, polynucleotide, orcomposition is attached to an antibody that binds to a targeted cell. Inanother embodiment, the peptide, polynucleotide, or composition isencapsulated in a liposome. Peptides can also be delivered using apolynucleotide that encodes a subject peptide. Any polynucleotide havinga nucleotide sequence that encodes a peptide of the invention iscontemplated within the scope of the invention. In one embodiment, thepolynucleotide is delivered to the cell where it is taken up and thepolynucleotide is transcribed into RNA and the RNA is translated intothe encoded peptide. Examples of viruses whose replication can beinhibited using the present invention include, but are not limited to,herpes viruses, poxviruses, and picornaviruses, such as vaccinia virus,EMC virus, influenza virus, herpes zoster virus, cytomegalovirus, andherpes simplex virus (e.g., HSV-1).

For the treatment of viral infections, the peptides, polynucleotides,and compositions of this invention can be administered to a patient inneed of treatment in combination with other antiviral substances. Theseother antiviral substances may be given at the same or different timesas the peptides, polynucleotides, and compositions of this invention.For example, the peptides, polynucleotides, and compositions of thepresent invention can be used in combination with one or more viralinhibitors such as interferons, and/or other drugs or antibodies, suchas IFNα, IFNβ, IFNγ, acyclovir (Zovirax), zidovudine (AZT), lamivudine(3TC), zanamivir (Relenza), oseltamivir (Tamiflu), valacyclovir(Valtrex), amantadine (Symmetrel), rimantadine (Flumadine), cidofovir(Vistide), foscarnet (Foscavir), ganciclovir (Cytovene), ribavirin(Virazole), nelfinavir (Viracept), ritonavir (Norvir), rifampin(Rifadin), and famciclovir (Famvir).

The subject invention also concerns methods for treating an oncologicaldisorder or an autoimmune disorder in a patient. In one embodiment, aneffective amount of a peptide, polynucleotide, or composition of thepresent invention that is an agonist of a type I IFN protein isadministered to a patient having an oncological disorder or anautoimmune disorder and who is in need of treatment thereof. The subjectinvention also concerns methods for inhibiting the growth of a cancercell by contacting the cell in vitro or in vivo with an effective amountof a peptide, polynucleotide, or composition of the present invention.The subject invention also concerns methods for activating an immunecell (e.g., T cell, NK cell, macrophage, etc.), and/or upregulatingantigen presentation to lymphocytes, and/or upregulating majorhistocompatibility complex (MHC) molecules, and/or activating a JAK/STATpathway, and/or activating TYK2 in a cell by contacting the cell invitro or in vivo with an effective amount of a peptide, polynucleotide,or composition of the present invention. In one embodiment, the peptidehas the amino acid sequence in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3,SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ ID NO:39, orSEQ ID NO:40, or a fragment or variant thereof that exhibits anticanceractivity. Methods of the invention can also further compriseadministering or contacting a cell with one or more compounds fortreating an oncological or autoimmune disorder. Such compounds can beadministered prior to, in conjunction with, and/or subsequent toadministration of a peptide, polynucleotide, and/or composition of thepresent invention. Methods of the invention can optionally includeidentifying a patient who is or may be in need of treatment of anoncological or autoimmune disorder. The patient can be a human or othermammal, such as a primate (monkey, chimpanzee, ape, etc.), dog, cat,cow, pig, or horse, or other animals having an oncological disorder.Means for administering and formulating peptides, polynucleotides, orcompositions of the invention for administration to a patient are knownin the art, examples of which are described herein. Autoimmune disorderswithin the scope of the invention include, but are not limited to,multiple sclerosis and rheumatoid arthritis. In one embodiment, ahuIFNβ1(100-187) (SEQ ID NO:2) peptide or huIFNβ1(150-187) (SEQ IDNO:39) peptide, or a polynucleotide encoding the peptide, is used totreat a person or animal having multiple sclerosis. Oncologicaldisorders within the scope of the invention include, but are not limitedto, cancer and/or tumors of the anus, bile duct, bladder, bone, bonemarrow, bowel (including colon and rectum), breast, eye, gall bladder,kidney, mouth, larynx, esophagus, stomach, testis, cervix, head, neck,ovary, lung, mesothelioma, neuroendocrine, penis, skin, spinal cord,thyroid, vagina, vulva, uterus, liver, muscle, pancreas, prostate, bloodcells (including lymphocytes and other immune system cells), and brain.Specific cancers contemplated for treatment with the present inventioninclude carcinomas, Kaposi's sarcoma, melanoma, mesothelioma, softtissue sarcoma, pancreatic cancer, lung cancer, leukemia (hairy cell,acute lymphoblastic, acute myeloid, chronic lymphocytic, chronicmyeloid, and other), and lymphoma (Hodgkin's and non-Hodgkin's), andfollicular lymphoma, and multiple myeloma. In one embodiment, a huIFNα2(SEQ ID NO:5) peptide, or a polynucleotide encoding the peptide, is usedto treat a person or animal having a melanoma.

Examples of cancers that can be treated according to the presentinvention are listed in Table 3.

TABLE 3 Examples of Cancer Types Acute Lymphoblastic Leukemia, AdultHairy Cell Leukemia Acute Lymphoblastic Leukemia, Head and Neck CancerChildhood Hepatocellular (Liver) Cancer, Adult Acute Myeloid Leukemia,Adult (Primary) Acute Myeloid Leukemia, Childhood Hepatocellular (Liver)Cancer, Childhood Adrenocortical Carcinoma (Primary) AdrenocorticalCarcinoma, Childhood Hodgkin's Lymphoma, Adult AIDS-Related CancersHodgkin's Lymphoma, Childhood AIDS-Related Lymphoma Hodgkin's LymphomaDuring Pregnancy Anal Cancer Hypopharyngeal Cancer Astrocytoma,Childhood Cerebellar Hypothalamic and Visual Pathway Glioma,Astrocytoma, Childhood Cerebral Childhood Basal Cell CarcinomaIntraocular Melanoma Bile Duct Cancer, Extrahepatic Islet Cell Carcinoma(Endocrine Pancreas) Bladder Cancer Kaposi's Sarcoma Bladder Cancer,Childhood Kidney (Renal Cell) Cancer Bone Cancer, Osteosarcoma/MalignantKidney Cancer, Childhood Fibrous Histiocytoma Laryngeal Cancer BrainStem Glioma, Childhood Laryngeal Cancer, Childhood Brain Tumor, AdultLeukemia, Acute Lymphoblastic, Adult Brain Tumor, Brain Stem Glioma,Leukemia, Acute Lymphoblastic, Childhood Childhood Leukemia, AcuteMyeloid, Adult Brain Tumor, Cerebellar Astrocytoma, Leukemia, AcuteMyeloid, Childhood Childhood Leukemia, Chronic Lymphocytic Brain Tumor,Cerebral Leukemia, Chronic Myelogenous Astrocytoma/Malignant Glioma,Leukemia, Hairy Cell Childhood Lip and Oral Cavity Cancer Brain Tumor,Ependymoma, Childhood Liver Cancer, Adult (Primary) Brain Tumor,Medulloblastoma, Liver Cancer, Childhood (Primary) Childhood LungCancer, Non-Small Cell Brain Tumor, Supratentorial Primitive LungCancer, Small Cell Neuroectodermal Tumors, Childhood Lymphoma,AIDS-Related Brain Tumor, Visual Pathway and Lymphoma, Burkitt'sHypothalamic Glioma, Childhood Lymphoma, Cutaneous T-Cell, see MycosisBrain Tumor, Childhood Fungoides and Sézary Syndrome Breast CancerLymphoma, Hodgkin's, Adult Breast Cancer, Childhood Lymphoma, Hodgkin's,Childhood Breast Cancer, Male Lymphoma, Hodgkin's During PregnancyBronchial Adenomas/Carcinoids, Lymphoma, Non-Hodgkin's, Adult ChildhoodLymphoma, Non-Hodgkin's, Childhood Burkitt's Lymphoma Lymphoma,Non-Hodgkin's During Carcinoid Tumor, Childhood Pregnancy CarcinoidTumor, Gastrointestinal Lymphoma, Primary Central Nervous SystemCarcinoma of Unknown Primary Macroglobulinemia, Waldenström's CentralNervous System Lymphoma, Malignant Fibrous Histiocytoma of PrimaryBone/Osteosarcoma Cerebellar Astrocytoma, Childhood Medulloblastoma,Childhood Cerebral Astrocytoma/Malignant Melanoma Glioma, ChildhoodMelanoma, Intraocular (Eye) Cervical Cancer Merkel Cell CarcinomaChildhood Cancers Mesothelioma, Adult Malignant Chronic LymphocyticLeukemia Mesothelioma, Childhood Chronic Myelogenous Leukemia MetastaticSquamous Neck Cancer with Chronic Myeloproliferative Disorders OccultPrimary Colon Cancer Multiple Endocrine Neoplasia Syndrome, ColorectalCancer, Childhood Childhood Cutaneous T-Cell Lymphoma, see MultipleMyeloma/Plasma Cell Neoplasm Mycosis Fungoides and Sézary MycosisFungoides Syndrome Myelodysplastic Syndromes Endometrial CancerMyelodysplastic/Myeloproliferative Diseases Ependymoma, ChildhoodMyelogenous Leukemia, Chronic Esophageal Cancer Myeloid Leukemia, AdultAcute Esophageal Cancer, Childhood Myeloid Leukemia, Childhood AcuteEwing's Family of Tumors Myeloma, Multiple Extracranial Germ Cell Tumor,Myeloproliferative Disorders, Chronic Childhood Nasal Cavity andParanasal Sinus Cancer Extragonadal Germ Cell Tumor NasopharyngealCancer Extrahepatic Bile Duct Cancer Nasopharyngeal Cancer, ChildhoodEye Cancer, Intraocular Melanoma Neuroblastoma Eye Cancer,Retinoblastoma Non-Hodgkin's Lymphoma, Adult Gallbladder CancerNon-Hodgkin's Lymphoma, Childhood Gastric (Stomach) Cancer Non-Hodgkin'sLymphoma During Pregnancy Gastric (Stomach) Cancer, Childhood Non-SmallCell Lung Cancer Gastrointestinal Carcinoid Tumor Oral Cancer, ChildhoodGerm Cell Tumor, Extracranial, Oral Cavity Cancer, Lip and ChildhoodOropharyngeal Cancer Germ Cell Tumor, ExtragonadalOsteosarcoma/Malignant Fibrous Germ Cell Tumor, Ovarian Histiocytoma ofBone Gestational Trophoblastic Tumor Ovarian Cancer, Childhood Glioma,Adult Ovarian Epithelial Cancer Glioma, Childhood Brain Stem OvarianGerm Cell Tumor Glioma, Childhood Cerebral Ovarian Low MalignantPotential Tumor Astrocytoma Pancreatic Cancer Glioma, Childhood VisualPathway and Pancreatic Cancer, Childhood Hypothalamic Pancreatic Cancer,Islet Cell Skin Cancer (Melanoma) Paranasal Sinus and Nasal CavityCancer Skin Carcinoma, Merkel Cell Parathyroid Cancer Small Cell LungCancer Penile Cancer Small Intestine Cancer Pheochromocytoma Soft TissueSarcoma, Adult Pineoblastoma and Supratentorial Primitive Soft TissueSarcoma, Childhood Neuroectodermal Tumors, Childhood Squamous CellCarcinoma, see Skin Pituitary Tumor Cancer (non-Melanoma) Plasma CellNeoplasm/Multiple Myeloma Squamous Neck Cancer with OccultPleuropulmonary Blastoma Primary, Metastatic Pregnancy and Breast CancerStomach (Gastric) Cancer Pregnancy and Hodgkin's Lymphoma Stomach(Gastric) Cancer, Childhood Pregnancy and Non-Hodgkin's LymphomaSupratentorial Primitive Primary Central Nervous System LymphomaNeuroectodermal Tumors, Childhood Prostate Cancer T-Cell Lymphoma,Cutaneous, see Rectal Cancer Mycosis Fungoides and Sézary Renal Cell(Kidney) Cancer Syndrome Renal Cell (Kidney) Cancer, ChildhoodTesticular Cancer Renal Pelvis and Ureter, Transitional Cell Thymoma,Childhood Cancer Thymoma and Thymic Carcinoma Retinoblastoma ThyroidCancer Rhabdomyosarcoma, Childhood Thyroid Cancer, Childhood SalivaryGland Cancer Transitional Cell Cancer of the Renal Salivary GlandCancer, Childhood Pelvis and Ureter Sarcoma, Ewing's Family of TumorsTrophoblastic Tumor, Gestational Sarcoma, Kaposi's Unknown Primary Site,Carcinoma of, Sarcoma, Soft Tissue, Adult Adult Sarcoma, Soft Tissue,Childhood Unknown Primary Site, Cancer of, Sarcoma, Uterine ChildhoodSezary Syndrome Unusual Cancers of Childhood Skin Cancer (non-Melanoma)Ureter and Renal Pelvis, Transitional Skin Cancer, Childhood Cell CancerUrethral Cancer Uterine Cancer, Endometrial Uterine Sarcoma VaginalCancer Visual Pathway and Hypothalamic Glioma, Childhood Vulvar CancerWaldenström's Macroglobulinemia Wilms' Tumor

For the treatment of oncological disorders, the peptides,polynucleotides, and compositions of this invention can be administeredto a patient in need of treatment in combination with other antitumor oranticancer substances and/or with radiation and/or photodynamic therapyand/or with surgical treatment to remove a tumor. These other substancesor treatments may be given at the same as or at different times from thepeptides, polynucleotides, and compositions of this invention. Forexample, the peptides, polynucleotides, and compositions of the presentinvention can be used in combination with mitotic inhibitors such astaxol or vinblastine, alkylating agents such as cyclophosamide orifosfamide, antimetabolites such as 5-fluorouracil or hydroxyurea, DNAintercalators such as adriamycin or bleomycin, topoisomerase inhibitorssuch as etoposide or camptothecin, antiangiogenic agents such asangiostatin, antiestrogens such as tamoxifen, and/or other anti-cancerdrugs or antibodies, such as, for example, GLEEVEC (NovartisPharmaceuticals Corporation) and HERCEPTIN (Genentech, Inc.),respectively. Peptides, polynucleotides, and compositions of theinvention can be used in combination with proteasome inhibitors,including, but not limited to, Bortezomib, Carfilzomib, andSalinosporamide A. The subject invention also concerns methods forinhibiting the growth of a cancer cell by contacting the cell in vitroor in vivo with an effective amount of a peptide, polynucleotide, orcomposition of the present invention.

Many tumors and cancers have viral genome present in the tumor or cancercells. For example, Epstein-Barr Virus (EBV) is associated with a numberof mammalian malignancies. The peptides, polynucleotides, andcompositions of the subject invention can also be used alone or incombination with anticancer or antiviral agents, such as ganciclovir,azidothymidine (AZT), lamivudine (3TC), etc., to treat patients infectedwith a virus that can cause cellular transformation and/or to treatpatients having a tumor or cancer that is associated with the presenceof viral genome in the cells.

The methods of the present invention can be used with humans and otheranimals. The other animals contemplated within the scope of theinvention include domesticated, agricultural, or zoo- orcircus-maintained animals. Domesticated animals include, for example,dogs, cats, rabbits, ferrets, guinea pigs, hamsters, pigs, monkeys orother primates, and gerbils. Agricultural animals include, for example,horses, mules, donkeys, burros, cattle, cows, pigs, sheep, andalligators. Zoo- or circus-maintained animals include, for example,lions, tigers, bears, camels, giraffes, hippopotamuses, andrhinoceroses.

In one embodiment, one or more of the peptides of the subject inventioncan be provided in the form of a multiple peptide construct. Such aconstruct can be designed so that multiple peptides are linked to eachother by intervening moieties wherein the intervening moieties aresubsequently cleaved or removed following administration of the multiplepeptide construct to a patient. Methods for constructing multiplepeptide constructs are known in the art. For example, peptides of thepresent invention can be provided in the form of a multiple antigenicpeptide (MAP) construct. The preparation of MAP constructs has beendescribed in Tam (1988). MAP constructs utilize a core matrix of lysineresidues onto which multiple copies of an immunogen are synthesized.Multiple MAP constructs, each containing different peptides, can beprepared and administered in accordance with methods of the presentinvention. In another embodiment, a multiple peptide construct can beprepared by preparing the subject peptides having at least one metalchelating amino acid incorporated therein, preferably at the aminoand/or carboxy terminal of the peptide as described, for example, inU.S. Pat. No. 5,763,585. The peptides are then contacted with a solidsupport having attached thereto a metal ion specific for the metalchelating amino acid of the peptide. A multiple peptide construct of theinvention can provide multiple copies of the exact same peptide,including variants or fragments of a subject peptide, or copies ofdifferent peptides of the subject invention.

Therapeutic application of the subject peptides, polynucleotides, andcompositions containing them, can be accomplished by any suitabletherapeutic method and technique presently or prospectively known tothose skilled in the art. The peptides and polynucleotides can beadministered by any suitable route known in the art including, forexample, oral, nasal, rectal, parenteral, subcutaneous, or intravenousroutes of administration. Administration of the peptides andpolynucleotides of the invention can be continuous or at distinctintervals as can be readily determined by a person skilled in the art.

Compounds and compositions useful in the subject invention can beformulated according to known methods for preparing pharmaceuticallyuseful compositions. Formulations are described in detail in a number ofsources which are well known and readily available to those skilled inthe art. For example, Remington's Pharmaceutical Science by E.W. Martindescribes formulations which can be used in connection with the subjectinvention. In general, the compositions of the subject invention will beformulated such that an effective amount of the bioactive peptide orpolynucleotide is combined with a suitable carrier in order tofacilitate effective administration of the composition. The compositionsused in the present methods can also be in a variety of forms. Theseinclude, for example, solid, semi-solid, and liquid dosage forms, suchas tablets, pills, powders, liquid solutions or suspension,suppositories, injectable and infusible solutions, and sprays. Thepreferred form depends on the intended mode of administration andtherapeutic application. The compositions also preferably includeconventional pharmaceutically acceptable carriers and diluents which areknown to those skilled in the art. Examples of carriers or diluents foruse with the subject peptides and polynucleotides include, but are notlimited to, water, saline, oils including mineral oil, ethanol, dimethylsulfoxide, gelatin, cyclodextrans, magnesium stearate, dextrose,cellulose, sugars, calcium carbonate, glycerol, alumina, starch, andequivalent carriers and diluents, or mixtures of any of these.Formulations of the peptide or polynucleotide of the invention can alsocomprise suspension agents, protectants, lubricants, buffers,preservatives, and stabilizers. To provide for the administration ofsuch dosages for the desired therapeutic treatment, pharmaceuticalcompositions of the invention will advantageously comprise between about0.1% and 45%, and especially, 1 and 15% by weight of the total of one ormore of the peptide or polynucleotide based on the weight of the totalcomposition including carrier or diluent.

The peptides, polynucleotides, and compositions of the subject inventioncan also be administered utilizing liposome technology, slow releasecapsules, implantable pumps, and biodegradable containers. Thesedelivery methods can, advantageously, provide a uniform dosage over anextended period of time.

The subject peptides and polynucleotides can also be modified by theaddition of chemical groups, such as PEG (polyethylene glycol).PEGylated peptides typically generate less of an immunogenic responseand exhibit extended half-lives in vivo in comparison to peptides thatare not PEGylated when administered in vivo. Methods for PEGylatingproteins and peptides known in the art (see, for example, U.S. Pat. No.4,179,337). The subject peptides and polynucleotides can also bemodified to improve cell membrane permeability. In one embodiment, cellmembrane permeability can be improved by attaching a lipophilic moiety,such as a steroid, to the peptide or polynucleotide. In anotherembodiment, peptides and polynucleotides of the invention comprise acell-penetrating peptide (CPP). CPPs are typically short peptides thatare highly cationic and typically include several arginine and/or lysineamino acids. CPPs can be classified as hydrophilic, amphiphilic, orperiodic sequence. In one embodiment, a CPP is provided at the terminusof a peptide or polynucleotide. Examples of CPPs include, but are notlimited to penetratin or antenapedia PTD (RQIKWFQNRRMKWKK) (SEQ IDNO:19), TAT (YGRKKRRQRRR) (SEQ ID NO:20), SynB1 (RGGRLSYSRRRFSTSTGR)(SEQ ID NO:21), SynB3 (RRLSYSRRRF) (SEQ ID NO:22), PTD-4 (PIRRRKKLRRLK)(SEQ ID NO:23), PTD-5 (RRQRRTSKLMKR) (SEQ ID NO:24), FHV Coat-(35-49)(RRRRNRTRRNRRRVR) (SEQ ID NO:25), BMV Gag-(7-25) (KMTRAQRRAAARRNRWTAR)(SEQ ID NO:26), HTLV-II Rex-(4-16) (TRRQRTRRARRNR) (SEQ ID NO:27), D-Tat(GRKKRRQRRRPPQ) (SEQ ID NO:28), R9-Tat (GRRRRRRRRRPPQ) (SEQ ID NO:29),Transportan (GWTLNSAGYLLGKINLKALAALAKKIL) (SEQ ID NO:30) chimera, MAP(KLALKLALKLALALKLA) (SEQ ID NO:31), SBP (MGLGLHLLVLAAALQGAWSQPKKKRKV)(SEQ ID NO:32), FBP (GALFLGWLGAAGSTMGAWSQPKKKRKV) (SEQ ID NO:33), MPG(ac-GALFLGFLGAAGSTMGAWSQPKKKRKV-cya) (SEQ ID NO:34), MPG^((ΔNLS))(ac-GALFLGFLGAAGSTMGAWSQPKSKRKV-cya) (SEQ ID NO:35), Pep-1(ac-KETWWETWWTEWSQPKKKRKV-cya) (SEQ ID NO:36), and Pep-2(ac-KETWFETWFTEWSQPKKKRKV-cya) (SEQ ID NO:37). Other CPPs can have onlyarginine (R) or only lysine (K) amino acids, e.g., having a formula(R)_(n) or (K)_(n), where n=an integer from 3 to 20. Other groups knownin the art for providing for cell membrane permeability can be linked topeptides and polynucleotides of the present invention.

The subject invention also concerns a packaged dosage formulationcomprising in one or more containers at least one peptide,polynucleotide, and/or composition of the subject invention formulatedin a pharmaceutically acceptable dosage. The package can containdiscrete quantities of the dosage formulation, such as tablet, capsules,lozenge, and powders. The quantity of peptide and/or polynucleotide in adosage formulation and that can be administered to a patient can varyfrom about 1 mg to about 5000 mg, or about 1 mg to about 2000 mg, ormore typically about 1 mg to about 500 mg, or about 5 mg to about 250mg, or about 10 mg to about 100 mg.

The subject invention also concerns kits comprising one or morepeptides, polynucleotides, compositions, compounds, or molecules of thepresent invention in one or more containers. In one embodiment, a kitcontains a peptide, polynucleotide, and/or composition of the presentinvention. In a specific embodiment, a kit comprises a peptidecomprising the amino acid sequence shown in SEQ ID NO:1, SEQ ID NO:2,SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ IDNO:39, or SEQ ID NO:40, or a fragment or variant of the peptide thatexhibits substantially the same activity as the full-length non-variantpeptide. A kit of the invention can also comprise one or more antiviralcompounds, biological molecules, or drugs and/or one or more type I IFNpeptide mimetics. In one embodiment, the biological molecule is one ormore of IFNα, IFNβ, or IFNγ. In one embodiment, in addition to apeptide, polynucleotide, composition, or compound of the invention, akit also comprises one or more peptides of SEQ ID NO:7 (MuIFNγ(95-132))and/or SEQ ID NO:8 (huIFNγ(95-134)), and/or SEQ ID NO:9 (Tkip peptide),and/or SEQ ID NO:10, or a fragment or variant thereof that exhibitsantiviral activity. In one embodiment, a kit comprises one or more ofIFNα, IFNβ, IFNγ, acyclovir (Zovirax), zidovudine (AZT), lamivudine(3TC), zanamivir (Relenza), oseltamivir (Tamiflu), valacyclovir(Valtrex), amantadine (Symmetrel), rimantadine (Flumadine), cidofovir(Vistide), foscarnet (Foscavir), ganciclovir (Cytovene), ribavirin(Virazole), nelfinavir (Viracept), ritonavir (Norvir), rifampin(Rifadin), and famciclovir (Famvir). In another embodiment, a kitcomprises one or more of mitotic inhibitors such as taxol orvinblastine, alkylating agents such as cyclophosamide or ifosfamide,antimetabolites such as 5-fluorouracil or hydroxyurea, DNA intercalatorssuch as adriamycin or bleomycin, topoisomerase inhibitors such asetoposide or camptothecin, antiangiogenic agents such as angiostatin,antiestrogens such as tamoxifen, and/or other anti-cancer drugs orantibodies, such as, for example, GLEEVEC (Novartis PharmaceuticalsCorporation) and HERCEPTIN (Genentech, Inc.), respectively.

In one embodiment, a kit of the invention includes instructions orpackaging materials that describe how to administer a peptide,polynucleotide, compositions, compounds, or molecules of the kit.Containers of the kit can be of any suitable material, e.g., glass,plastic, metal, etc., and of any suitable size, shape, or configuration.In one embodiment, a peptide, polynucleotide, compositions, compounds,or molecules of the invention is provided in the kit as a solid, such asa tablet, pill, or powder form. In another embodiment, a peptide,polynucleotide, compositions, compounds, or molecules of the inventionis provided in the kit as a liquid or solution. In one embodiment, thekit comprises an ampoule or syringe containing a peptide,polynucleotide, compositions, compounds, or molecules of the inventionin liquid or solution form.

The subject invention also concerns methods for inhibiting type I IFNcell activation and/or intracellular signaling. In one embodiment, aninhibitor of an IFNAR is provided in a cell. In a further embodiment,the IFNAR is IFNAR1 or IFNAR2. The cell can be a mammalian cell, such asa human cell. In one embodiment, the cell is infected with a virus. Anysuitable inhibitor that can inhibit the function of an IFNAR iscontemplated within the scope of the invention. Examples of inhibitorsinclude, but are not limited to, antibodies (and antigen bindingfragments thereof) and other compounds or agents that bind to an IFNAR.

Materials and Methods for Examples 1-6 Cell Culture and Abs

WISH and Daudi cells were purchased from American Type CultureCollection (ATCC) and were grown in MEME and RPMI (Sigma-Aldrich),respectively, with 10% FBS and antibiotics. For all experiments, cellswere serum starved for at least 4 hours, washed twice with PBS and thengiven serum free media with or without 1,000 U/ml IFNα2 (Calbiochem) orIFN. The following polyclonal antisera were purchased from Santa CruzBiotech: IFNAR1, IFNAR2, STAT1, pSTAT1, STAT2, pSTAT2, TYK2, pTYK2,normal rabbit IgG, β-Tubulin, β-Lamin, and Histone H3. The followingpolyclonal antisera were purchased from Active Motif: H3K9ac andH3K9me3. Additional Abs to TYK2 and IFNAR1 were also purchased from BDBioscience and Epitomics, respectively. We produced the antibody totyrosine phosphorylated histone H3 by immunization of rabbits withhistone H3 peptide, ³³GGVKKPHRpYRPGTVALREIR (SEQ ID NO:13), with aphosphate at tyrosine 41. We tested antibodies to some proteins fromdifferent sources to monitor the specificity.

Chromatin Immunoprecipitation (ChIP) Assay

WISH cells were treated or not with type I IFN for 1 hr. Cells were thenwashed twice with cold PBS and treated with 1% formaldehyde for 10 minat 37° C. The rest of the procedure was conducted using the ChIP kitfrom Millipore, as per the manufacturer's protocol. Sonication wasconducted to get DNA fragments of ˜500 bp. Control IgG, or differentAbs, were used for each immunoprecipitation as indicated. DNA fragmentseluted were used for PCR with the following primers that spanned theISRE element in their promoters. Human OAS1 promoter region wasamplified with the primers 5′-CATTGACAGGAGAGAGAGTG-3′ (SEQ ID NO:14)(−147 to −133) and 5′-TCAGGGGAGTGTCTGATTTG-3′ (SEQ ID NO:15) (−17 to+3). As a control, PCR was conducted with the primers from the humanβ-actin promoter 5′-CTCGCTCTCGCTCTTTTTTTTTTTC-3′ (SEQ ID NO:16) (−967 to−941) and 5′-CTCGAGCCATAAAAGGCAACT-3′ (SEQ ID NO:17) (−844 to −864). ThePCR conditions were as follows: heating at 94° C. for 5 min, followed by35 cycles at 94° C. for 15 sec, 60° C. for 30 sec, and 68° C. for 15sec. This was followed by annealing at 68° C. for 5 min. Following ChIPwith the indicated Abs, the DNA protein complex was used to elute theassociated proteins by boiling with the electrophoresis buffer and wasanalyzed by Western blotting as mentioned before (Noon-Song et al.,2011).

Isolation of Nuclei

IFN treated WISH cells were washed twice in cold PBS, removed byscraping in lysis buffer (10 mM HEPES pH 7.9, 100 mM KCl, 1% TritonX-100, 1 mM NaF, 1 mM Na₃VO₄, 2 mM MgCl₂, 1 mM DTT, and 1 mM PMSF), andpelleted by low speed centrifugation. The supernatant was saved ascytoplasmic fraction. The pellet containing intact nuclei, was gentlyresuspended in lysis buffer. The centrifugation, re-suspension, anddecanting was then repeated twice more. Isolated nuclei were confirmedby trypan blue staining.

Western Blot Analysis and Immunoprecipitation Cells were washed with PBSand harvested in lysis buffer (10 mM HEPES pH 7.9, 100 mM KCl, 1% TritonX-100, 1 mM NaF, 1 mM Na₃VO₄, 2 mM MgCl₂, 1 mM DTT, and 1 mM PMSF).Whole cell lysate was generated via sonication on ice and insolublematerial removed via centrifugation at 14 k rpm for 10 min at 4° C.Protein concentration was measured using 660 nm protein assay reagent(Pierce). Protein (10 μg each) was electrophoresed on an acrylamide gel,transferred to PVDF membrane, and probed with the indicated Abs.HRP-conjugated secondary Abs were then added and detection was conductedby chemiluminescence (Pierce). Immunoprecipitation was conducted byincubating specific Abs with equal amounts of lysate, followed byincubation with Protein A-Agarose (Santa Cruz Biotech) for at least 2hours. Precipitated material was sedimented and washed thrice with PBS.Pellets were taken in electrophoresis buffer, boiled and loaded on anacrylamide gel, transferred and probed with antibodies indicated.

Expression and Purification of Type I IFN Mimetics

Type I IFN mimetics were expressed as follows. The coding sequence forhuman IFNα1, IFNα1 (69-189), preceded by nine arginine (R9) residues(for cell penetration) was inserted in the bacterial expression vector,pET30a+. The coding sequence for human IFNβ, IFNβ(100-187) preceded byR9 was similarly inserted into pET30a+. As controls, the humanIFNα1(69-189) or IFNβ(100-187) without the R9 were also inserted inpET30a+. E. coli BL21 (DE3) Rosetta strain was used to transform theexpression sequence in pET30a+. After the bacterial growth had reachedthe mid-log phase, induction with 0.5 mM IPTG was carried out and growthcontinued for 4 hours. The proteins were purified by using the Ni-NTAHis Bind Resin (Novagen). The His tag was removed by digesting withenterokinase. The purity of the protein was assessed by SDS-PAGEanalysis and coomassie blue staining.

GFP Fusion Constructs and Microscopy

The coding sequence from IFNτ, IFNAR1, or IFNAR2 was used to generate aPCR product that was fused in frame with the C terminus of humanizedrGFP in the plasmid phrGFPII-C (Stratagene). WISH cells that were grownon coverslips to near 30% confluency in a 35 mm dish were transfectedusing lipofectamine (Invitrogen Life Technologies), with 3 μg of theempty vector or the IFNτ fused GFP vector. IFNAR1 or IFNAR2 sequencesfused to GFP were similarly transfected. Where indicated, IFNτ was addedat 1,000 U/ml. Next day, cells were fixed with 2% paraformaldehyde inPBS, mounted on a slide, and viewed in a Zeiss Axiovert Zoom confocalmicroscope using LSM Pascal software, as described before (Ahmed andJohnson, 2006).

Antiviral Assay

Antiviral assays were performed by using a cytopathic effect (CPE)reduction assay using encephalomyocarditis (EMC) virus. WISH cells(40,000 per well in a microtiter dish) were grown overnight.IFNα1(69-189)R9, IFNβ(100-187)R9, or their controls without the R9sequence were added to cells at the concentrations indicated for 4 hr,followed by infection with EMCV (moi=0.01). Virus was washed after onehr and cells were grown overnight. Cells were stained with crystalviolet and read in a microtiter plate at 550 nm.

Induction of EAE, Evaluation of Clinical Disease, and Administration ofPeptides

Female SJL/J mice (6 to 8 weeks old) were purchased from JacksonLaboratories (Bar Harbor, Me.) and housed in standard SPF facilities. Onday 1, SJL/J mice were injected with 300 μg/mouse bovine myelin basicprotein (Invitrogen) emulsified in Complete Freund's Adjuvant with 8mg/ml H37Ra Mycobacterium tuberculosis (Sigma-Aldrich) and injectedsubcutaneously into two sites at the base of the tail along with 400ng/mouse pertussis toxin (List Biological Laboratories Inc) in PBS i.p.On day 3, the pertussis toxin injection was repeated (Jager et al.,2011). Beginning on day 12 post-immunization, after lymphocyteinfiltration of the CNS had begun, mice were administered the followingtreatments or peptides every other day via i.p. injection in 100 μlfinal volume: PBS, IFNα1(69-189)R9 (15 μg/mouse), or IFNα1(69-189) (15μg/mouse). The mice were monitored daily for signs of EAE and gradedaccording to the following scale: 0, normal; 1, loss of tail tone; 2,hind limb weakness; 3, paraparesis; 4, paraplegia; 5, moribund; and 6,death. The Institutional Animal Care and Use Committee at the Universityof Florida approved all of the animal protocols mentioned here.

All patents, patent applications, provisional applications, andpublications referred to or cited herein are incorporated by referencein their entirety, including all figures and tables, to the extent theyare not inconsistent with the explicit teachings of this specification.

Following are examples that illustrate procedures for practicing theinvention. These examples should not be construed as limiting. Allpercentages are by weight and all solvent mixture proportions are byvolume unless otherwise noted.

Example 1 Activated TYK2, JAK1, and Interferon Alpha/Beta ReceptorSubunits (IFNAR1 and IFNAR2) in the Nucleus of Type I IFN Treated Cells

We have recently shown that treatment of WISH cells with IFNγ resultedin the presence of activated JAK1 and JAK2 in the nucleus (Noon-Song etal., 2011). We thus treated WISH cells with type I IFNs IFNα2 and IFNτ,which have similar specific antiviral activities, but IFNα2 with muchmore potent apoptosis activity (Subramaniam et al., 1995). The focus wason the presence of activated TYK2, JAK1, and receptor subunits IFNAR1and IFNAR2 in the nucleus of cells treated with type I IFNs. At aconcentration of 1000 U/ml, IFNα2 treatment resulted in the presence ofboth phosphorylated (activated) JAKs, pJAK1 and pTYK2, in the nucleus(FIG. 1A). Nonphosphorylated TYK2 was constitutively present in thenucleus of untreated cells. Nonphosphorylated JAK1 was also present inthe nucleus (data not shown). IFNτ treatment similarly resulted in thepresence of pTYK2 in the nucleus (FIG. 1B). Both phosphorylated STAT1βand STAT2 were detected in the nucleus only after treatment of cellswith the IFNs (FIGS. 1A and 1B). To ascertain the purity of nuclearfractionations, β-tubulin and β-lamin were used as markers of nuclearand cytoplasmic fractions, respectively (FIGS. 1A, 1B, and 1C).

Focus on activated JAKs in the nucleus without context, although of someinterest, provides little insight into their role in specific geneactivation. Thus, we also examined the movement of type I IFN receptorsubunit IFNAR1 into the nucleus of WISH cells treated with the IFNs. Forboth IFNα2 (FIG. 1A) and IFNτ (FIG. 1B), IFN treatment resulted in thepresence of IFNAR1 in the nucleus. There were relatively low or traceamounts of IFNAR1 in the nucleus of untreated cells, which increasedseveral fold after treatment with IFNα2 or IFNτ. This is consistent witha low constitutive endogenous level of IFNβ in untreated cells (Takokaet al., 2000; Taniguchi and Takaoka, 2008). This constitutive IFNβ hasbeen shown to be important for priming cells for both induction of typeI IFNs and in enhancement of the cellular response to both IFNγ and typeI IFNs. We also determined that IFNAR2 similarly underwent nucleartranslocation in IFNτ treated WISH cells (FIG. 1C). The movement ofIFNAR1 and IFNAR2 into the nucleus along with the JAKs suggests anassociation of the two events. Consistent with these results, we haveidentified a functional nuclear localization sequence in IFNAR1(Subramaniam and Johnson, 2004) and IFNAR2 (²⁸³RKKK (SEQ ID NO:18);unpublished observation) and a putative NLS in TYK2 (Ragimbeau et al.,2001).

To further verify the movement of IFNAR1 and IFNAR2 into the nucleus ofIFN treated cells as well as to determine if the type I IFN similarlyunderwent nuclear import, we carried out confocal microscopy with GFPfusion proteins. Specifically, WISH cells were transfected separatelywith CMV promoter driven constructs of IFNτ, IFNAR1, or IFNAR2 fused toGFP. As control, WISH cells were also transfected with vector containingonly GFP. As shown in FIG. 2A, IFNτ-GFP treated cells showed anincreased presence of IFNτ-GFP in the nucleus, while control GFP waspresent throughout the cell. In IFNAR1-GFP transfected cells, treatmentwith IFNτ caused nuclear translocation, while untreated cells showed nopreference of IFNAR1-GFP for the nucleus as shown in FIG. 2B. IFNAR2-GFPwas similarly driven into the nucleus of cells treated with IFNτ asshown in FIG. 2C. Thus, the type I IFN IFNτ and receptor subunits IFNAR1and IFNAR2 all undergo increased nuclear translocation in cells treatedwith the IFN. Possible small amounts of IFNAR1 and IFNAR2 in the nucleusof untreated cells would probably be due to the constitutive endogenousIFNβ (Takoka et al., 2000; Taniguchi and Takaoka, 2008). These findingsdiffer from the IFNγ system in that IFNGR1 translocated to the nucleus,while the IFNGR2 receptor subunit remained in the plasma membranes afterIFNγ treatment of cells where it provided JAK2 to IFNGR1 (Szente et al.,1995). Thus, although similar in nuclear events, the type I and type IIIFN systems differ in terms of receptor movement.

Example 2 Recruitment of IFNAR1, TYK2, and STAT1, Along withPhosphorylation of Histone H3Y41 (H3pY41) at the ISRE in the PromoterRegion of the OAS1 Gene of Cells Treated with Type I IFN

To determine if the type I IFN players of FIG. 1 were specificallyrecruited to the promoter region of a gene activated by IFNα2 in cells,we performed ChIP assays. WISH cells were treated with 1000 U/ml of IFNτfor 1 hour and analyzed by ChIP of sonicated chromatin of approximately500-bp fragments of DNA, followed by PCR. Chromatin fragments wereimmunoprecipitated with antibodies to IFNAR1, histone H3 tyrosine 41(H3pY41), TYK2, and STAT1, followed by PCR of the OAS1 promoter regionextending from nucleotides −147 to 3. As a control, PCR product for thepromoter of β-actin gene, −967 to −844, was chosen for ChIP analysis.IgG did not interact with the promoter containing complex as a controlfor non-specific binding. As shown in FIG. 3, IFNAR1, H3pY41, TYK2, andSTAT1 were associated with the ISRE element of the OAS 1 promoter inIFNα2 treated cells. The β-actin gene is not activated by type I IFNsand ChIP analysis showed that receptor subunit IFNAR1, H3pY41, JAKs, andSTAT1 were not associated at its promoter after IFNτ treatment. Studiesof IFN signaling have tended to focus extensively on STATs whenexamining the promoter region of genes activated by IFN as well as byother factors that signal via the JAK/STAT pathway (Levy and Darnell,2002). The ChIP data here provide insight into the mechanism of specificgene activation as well as the associated H3pY41 epigenetic event of thetype I IFN signaling and suggest that STAT is but one player in thesecomplex events.

Example 3 TYK2 Associates with IFNAR1 in the Nucleus of Cells Treatedwith Type I IFN

The demonstration of activated JAK2V617F and cytokine activated JAK2 inthe nucleus of cells and their phosphorylation of H3Y41 (H3pY41) in thechromatin did not address the fact that epigenetic events such as thismust involve some mechanism of specificity (Dawson et al., 2009).JAK2V617F, for example, is associated with specific myeloproliferativedisorders and cytokine activation of wild type nuclear JAK2 isassociated with the specific biological effect of the particularcytokine We showed in FIG. 3 above that TYK2 and H3pY41 werespecifically associated with the OAS1 promoter in cells treated with atype I IFN. Since IFNAR1 is specific to type I IFN signaling and waspresent along with TYK2 at the OAS 1 promoter, we asked the question asto whether TYK2 and IFNAR1 were associated in the nucleus of cellstreated with a type I IFN, as this would suggest a basis of specificity.Accordingly, the human fibroblast cells were treated with 1000 U/ml ofIFNα2 for 30 min, after which the cells were lysed and nuclear andcytosolic fractions were isolated. The nuclear and cytoplasmic fractionswere IPed with antibody to IFNAR1 and Western blotted with antibodies toIFNAR1, TYK2, activated STAT1α (pSTAT1α), and H3pY41. As can be seen inFIG. 4, nuclear TYK2, pSTAT1α, and H3pY41 showed increased binding toIFNAR1 in IFNα2 treated cells. IgG treated control cells did not showsimilar association in whole cell extracts (data not shown). This isevidence that TYK2 as well as pSTAT1α do not function alone orindependently of the cytokine system whose function they are associatedwith in the nucleus at the level of gene activation.

Example 4 Specific Epigenetic Changes at the OAS 1 Promoter of CellsTreated with a Type I IFN

We showed by ChIP analysis that IFNτ treatment of cells resulted inspecific binding of IFNAR1, STAT1α, and TYK2 to the ISRE of the promoterof the OAS1 gene.

We examine here associated epigenetic changes by similar ChIP analysisat the OAS 1 promoter. FIG. 5A shows decreased trimethylated lysine 9 onhistone H3, H3K9me3, in the OAS1 promoter region of cells treated with1000 U/ml of IFNτ over 40 minutes. Acetylation of H3K9, H3K9ac, occurredconcomitantly over the same time span. Demethylation/acetylation of H3K9is associated with gene activation (Berger, 2007; Mehta et al., 2011).Related to this, phosphorylation of H3 at Y41, H3pY41, increased asH3K9me3 decreased over the same time period. Phosphorylation of H3Y41was confirmed by Western blot (FIG. 5B). By comparison, theconstitutively activated β-actin gene, which is not affected by IFN,showed constitutive H3K9ac, no H3pY41, and no H3 K9me3. The presence ofactivated JAKs at the OAS 1 region of type I IFN treated cells may berelated to H3Y41 phosphorylation which in turn could play a role in thedemethylation and acetylation of H3K9 at the promoter region of thegene. These observations suggest that the receptor/transcriptionfactor/JAK complex of type I IFN treated cells plays a key role inspecific gene activation, including the associated events ofheterochromatin modification.

Example 5 N-Terminal Truncated Type I IFNs Lose Extracellular Activitywhile Retaining Intracellular Activity. Evidence of Cytoplasmic Binding

In development of the IFNγ mimetics, we found that N-terminaltruncations of IFNγ to IFNγ(95-132) for mouse and IFNγ(95-134) for humanIFNγ resulted in loss of recognition of extracellular receptor (Szenteet al., 1996; Ahmed et al., 2005). These truncated IFNs were, however,active when introduced intracellularly via a palmitate group with fullantiviral activity (Ahmed et al., 2005). In order to determine if IFNα1and IFNβ possessed similar C-terminus function intracellularly whilelosing extracellular function, we expressed truncated IFNα1(69-189)R9and IFNβ (100-187)R9 with nine arginines (R9) for cell penetration in abacterial expression system and purified the polypeptides. As controls,we also expressed these truncations without R9. Both IFNα1(69-189)R9(FIG. 6A) and IFNβ(100-187)R9 (FIG. 6B) possessed antiviral activityagainst EMC virus, while the same constructs without R9 for cellpenetration lacked antiviral activity. R9 alone also lacked antiviralactivity (data not shown). This is consistent with previous studies thatshowed that intracellularly expressed IFNα possessed antiproliferativeand antiviral activity (Ahmed et al., 2001). The truncation studies,however, are not subject to the argument that somehow the intracellularIFN may have leaked out of the cell and interacted with theextracellular receptor domains, since the truncations were notfunctional in terms of extracellular induced antiviral activity.

Type I IFN is the treatment of choice for relapsing/remitting multiplesclerosis (MS) (National Multiple Sclerosis Society Bulletin, 2012), sowe tested IFNα1 (69-189)R9 for its ability to therapeutically treatSJL/J mice in experimental allergic encephalomyelitis (EAE), a mousemodel of MS. Immunization of mice with bovine myelin basic protein (MBP)where cellular infiltration into the CNS has occurred by day 12 was usedto test the truncated IFNs (Jager et al., 2011). IFNα(69-189)R9administration beginning at day 12 and every other day thereafterremitted with essentially complete therapeutic efficacy, while IFNα1(69-189) and PBS treated mice developed paraplegia (FIG. 6C).

The results presented here for induction of antiviral activity and EAEtherapy by cell-penetrating truncated type I IFNs are inexplicable inthe context of a model where the type I IFN exerts its effect solely byextracellular interaction with the receptor. The data are compatiblewith our IFNγ model where IFN after binding to receptor extracellulardomain goes on to bind to the cytoplasmic domain of receptor inconjunction with endocytic events (Subramaniam and Johnson, 2002). Thecomplex formation and the functional cytoplasmic activity of IFNtruncations thus show similarities to steroid signaling (Johnson et al.,2012).

Example 6

Specific gene activation by cytokines such as the IFNs is attributedsolely to the activated STATs (Levy and Darnell, 2002). In the case ofIFNγ signaling, interaction of IFNγ with receptor results inautoactivation of JAK1 and JAK2, which in turn activate STAT1α inconjunction with receptor subunit IFNGR1. Activated STAT 1α forms ahomodimer, dissociates from IFNGR1, and undergoes active nucleartransport via an unconventional nuclear localization sequence (NLS) thatassociates with the importin α/β proteins (Johnson et al., 2004). Thefact that STAT1α is activated by other cytokines in addition to IFNγwould suggest that STATs do not intrinsically contain the mechanism forspecific gene activation by a particular cytokine (Johnson et al., 2012;Johnson et al., 2004; Johnson and Ahmed, 2006). This is reinforced bythe fact that there are just seven STATs that function mostly ashomodimeric transcription factors for over 60 different cytokines,growth factors, and hormones (Johnson et al., 2012; Johnson et al.,2004; Johnson and Ahmed, 2006).

Recently, nuclear JAK2 has been shown to play an important role at theepigenetic level in gene activation. Mutant activated JAK2, JAK2V617F,was shown to be constitutively present in the nucleus of effector cellsof myeloproliferative disorders (Dawson et al., 2009). JAK2V617F wasshown to phosphorylate tyrosine 41 on histone H3 (H3Y41), which isassociated with gene activation. The constitutive activation ofJAK2V617F required association with hematopoietic receptors such as thatfor erythropoietin (EPOR) at the cytoplasmic domain (Lu et al., 2008).The mechanism of how JAK2V617F underwent nuclear translocation as wellas possible involvement of other proteins such as EPOR was notaddressed. It was also shown that wild-type JAK2 was constitutivelypresent in the nucleus of nonmyeloproliferative cell lines, but was onlyactivated after treatment of K562 cells with PDGF or LIF or treatment ofBaF3 cells with IL-3 (Dawson et al., 2009). As with JAK2V617F, themechanism by which nonphosphorylated and phosphorylated JAK2 enteredinto the nucleus was not addressed.

Phosphorylation of H3Y41 by activated nuclear JAK2 assigns a previouslyunknown function to a JAK kinase. The presence of JAKs in the nucleus,phosphorylated and unphosphorylated, was however previously known. JAK1,JAK2, and TYK2 have all previously been shown to be constitutivelypresent in the nucleus (Ragimbeau et al., 2001; Zouein et al., 2011;Nilsson et al., 2006). Activated JAK2 was shown to be present in growthhormone treated CHO cells that had been transfected with growth hormonereceptor (Lobie et al., 1996). These observations may not have receivedmuch attention as they were not obviously explainable in the context ofthe classical model of JAK/STAT signaling.

We have previously shown that IFNγ and one of its receptor subunits,IFNGR1, are translocated to the nucleus, together with activated STAT1αas one macromolecular complex via the classical importin-dependentpathway (Ahmed and Johnson, 2006). We have further shown that IFNγ andIFNGR1 are recruited to the IFNγ-activated genes (Noon-Song et al.,2011; Ahmed and Johnson, 2006). The direct association of IFNGR1 withthe promoter region of IFNγ-activated genes suggested atranscriptional/cotranscriptional role for IFNGR1 as well as itspossible role in determining the specificity of gene activation by IFNγ.

The role of activated JAKs in specific gene activation of IFNγ wasaddressed in the context of the above macromolecular complex. ChIPfollowed by PCR in IFNγ treated WISH cells showed association ofactivated JAK1 (pJAK1) and JAK2 (pJAK2) with the IFNγ/IFNGR1/pSTAT1αcomplex on the same DNA sequence of the 1RF-I gene promoter (Noon-Songet al., 2011). The β-actin gene, which is not activated by IFNγ, did notshow this association. Activated JAKs in the nucleus were associatedwith phosphorylation of H3Y41 in the GAS region of the IRF-1 promoter(Noon-Song et al., 2011). Unphosphorylated JAK2 was constitutivelypresent in the nucleus and was capable of undergoing activation in IFNγtreated cells, most likely via nuclear IFNGR1. The IFNγ studies ofactivated JAK2 in the nucleus suggest that it functions in the contextof the IFNγ/IFNGR1/pSTAT1α complex. This in turn provides a mechanismfor controlling or identifying specific chromatin regions for pJAK2activated epigenetic effects.

Our results here provide insight into type I IFN signaling in terms ofIFN/receptor/STAT/TYK2 nuclear complexes. We showed thatnonphosphorylated TYK2, like JAK2, is constitutively present in thenucleus. TYK2 is activated (pTYK2) in the nucleus only after interactionof type I IFN with the receptor complex, and, like pJAK2, phosphorylatedH3Y41 at a gene (OASI) that is activated by type I IFNs, while absentfrom an unrelated gene (β-actin). Thus, the epigenetic event of H3Y41phosphorylation is not unique to any particular JAK, but probablyinvolves the JAKs that are associated with the stimulating cytokine.

Both IFNAR1 and IFNAR2 underwent nuclear translocation in type I IFNtreated cells. This is in contrast to IFNγ where IFNGR2 remainedassociated with the cell membrane while IFNGR1 underwent nucleartranslocation as part of a complex as indicated above (Ahmed andJohnson, 2006; Ahmed et al., 2003). We showed that IFNGR2 provided JAK2to IFNGR1 via IFNγ induced increased binding affinity for IFNGR1 (Szenteet al., 1995). For type I IFNs, TYK2 is associated with IFNAR1 whileJAK1 is associated with IFNAR2 (Stark et al., 1998). After type I IFNtreatment, pTYK2 and probably pJAK1 undergo nuclear translocation as apart of macromolecular complex that contains IFNAR1 and IFNAR2. Similarto IFNγ, we also observed nuclear translocation of type I IFN, IFNτ, byconfocal microscopic analysis. Nuclear translocation of type I IFN hasbeen known for some time (Kushnaryov et al., 1986). This observationagain cannot be explained by the classical model of JAK/STAT signaling.

Since pTYK2 involvement in phosphorylation of H3Y41 was specific for agene that is induced by type I IFNs, the question arises as to whetherhistone associated demethylation and acetylation show similarspecificity. Focusing on trimethylated histone H3 lysine 9 (H3K9me3), weobserved that in type I IFN treated cells H3K9me3 underwentdemethylation in association with acetylation (H3K9ac) at the region ofthe OAS1 promoter. These changes in H3K9 are associated with geneactivation (Berger, 2007; Mehta et al., 2011). The association of IFNreceptors with pSTAT1α, pTYK2, and probably other factors in the regionof genes activated by IFN provides insight into the mechanism ofspecific gene activation, including associated phosphorylations,methylations, demethylations, and acetylations.

In a search for precedent, it seems that our study of both type I andtype II IFN signaling shares similarities to that of steroid receptor(SR) signaling. SRs are a major subset of nuclear receptors (Stanisic etal., 2010). Basically, synthesis of steroid hormones (SHs) occurs in theadrenal cortex and in gonads (Stanisic et al., 2010). Broadly, thecurrent model of SH signaling is as follows. In the absence of hormone,cytoplasmic SR monomers are associated with heat shock proteins (HSPs)and usually possess some basal level of phosphorylation (Stanisic etal., 2010). Upon binding of hormone, SRs dissociate from HSPs, dimerize,and translocate to the nucleus where they bind to hormone receptorelements (HREs) at genes that are activated by SHs. The complex of SH/SRrecruits a series of coactivators to both regulate target genetranscription as well as the associated epigenetic events that accompanygene expression. Site-specific phosphorylation of receptors occurssubsequent to hormone binding with varied kinetics, depending on thekinase and the target in the receptor complex. The kinases, while notthe only components of the receptor associated co-activator complexes,are important for their action on members of the receptor complex aswell as for specific epigenetic events of gene activation and thus acton histones as well as on members of the receptor complex.

Unlike SH/SR interaction, both type I and II IFN signaling initiateswith ligand binding to the receptor extracellular domain. However, wehave shown that IFNγ also binds to the cytoplasmic domain of receptorsubunit IFNGR1 during the process of endocytosis (Szente et al., 1995;Szente et al., 1996). We showed that the N-terminus of IFNγ played thekey role in recognition of IFNGR1 extracellular domain, while theC-terminus played the key role in binding to the cytoplasmic domain.This in turn led to development of IFNγ mimetics based on the C-terminus(Szente et al., 1996; Ahmed et al., 2007). We showed here thatN-terminus truncations of IFNα and IFNβ resulted in loss of signalingvia extracellular receptor interaction, while the same truncated IFNswith R9 attached for cell penetration possessed antiviral activity andanti-autoimmune function in EAE. These results would suggest that type IIFNs also interact with receptor cytoplasmic domain. Type I IFNcytoplasmic receptor interaction is probably more complex than that ofIFNγ where only the receptor subunit IFNGR1 undergoes endocytosis, whileboth IFNAR1 and IFNAR2 undergo endocytosis in type I IFN signaling. Thedemonstration of extracellular receptor interaction for IFNs isessentially the extra step in signaling compared to SHs, which interactdirectly with the cytoplasmic SR. In both systems we haveligand/receptor/coactivator complexes that undergo nucleartranslocation. The receptor complexes bind to promoter regions of genesthat they specifically activate. Thus, the results of this and previousstudies with IFNγ suggest that signaling by cytokines such as the IFNsis but a variation of steroid/steroid receptor signaling.

Materials and Methods for Examples 7 and 8 For FIG. 7 (Weight Loss) andTable 4 (Cell Counts): Measurement of IFN Toxicity

To measure toxicity induced by IFN treatment in vivo, mice (C57BL/6,n=3) were injected i.p. with IFNβ (10³ U/mouse), IFNα(69-189)R9 (2×10³U/mouse), IFNβ(100-187)R9 (2×10³ U/mouse), or PBS on alternate days.Mice were weighed daily until day 11 to see the effects of treatment onbody weight. On day 11, blood was drawn from facial vein and white bloodcell (WBC) counts were enumerated using a hemacytometer. DifferentialWBC counts were performed on Wright-Giemsa-stained blood smears.

For FIG. 8 (Apoptosis): Apoptosis Assay

Apoptosis on IFN and IFN mimetic treated cells was performed aspreviously described (Subramaniam et al., 1995). Briefly, WISH cells(150,000) were seeded in a 6 well plate and grown overnight. They werethen treated with type I IFN mimetics (100 U/ml), or parent IFNs (100U/ml) for 4 days. Cells were doubly stained with Annexin V and propidiumiodide (PI), using the reagents from Invitrogen, and analyzed by flowcytometry to measure the extent of apoptosis. The data shown indicatethe percentage of apoptosis based on cells staining for both Annexin Vand PI from the analysis of 10,000 cells.

For FIG. 9 (Antiviral Assay): Antiviral Assay

Antiviral assays were performed by using a cytopathic effect (CPE)reduction assay using vesicular stomatitis virus (VSV). L929 cells(40,000 per well in a microtiter dish) were grown overnight.Lipo-IFNα1(152-189), lipo-IFNβ(150-187), or lipo-IFNτ(156-195) wereadded to cells at the concentrations indicated for 4 hr, followed byinfection with VSV (moi=0.1). Virus was washed after one hr and cellswere grown overnight. Cells were stained with crystal violet and read ina microtiter plate at 550 nm. Parent IFNα1 was used at the concentrationindicated. “Scr” refers to a scrambled peptide corresponding toIFNτ(156-195).

For FIG. 10 (Antiviral Assay):

Antiviral assay was carried out using encephalomyocarditis (EMC) virusgrowing on WISH cells. Antiviral assays were performed by using acytopathic effect (CPE) reduction assay using encephalomyocarditis (EMC)virus growing on WISH cells. WISH cells (40,000 per well in a microtiterdish) were grown overnight. Lipo-IFNα1 (152-189), lipo-IFNβ(150-187), orlipo-IFNτ(156-195) were added to cells at the concentrations indicatedfor 4 hr, followed by infection with EMC (moi=0.1). Virus was washedafter one hr and cells were grown overnight. Cells were stained withcrystal violet and read in a microtiter plate at 550 nm. Parent IFNα1was used at the concentration indicated. “Scr” refers to a scrambledpeptide corresponding to IFNτ(156-195).

For FIG. 11 (Antiviral Assay):

Antiviral assay was carried out using vaccinia virus growing on BSC-40cells. After 48 hrs of infection, cells were stained with crystal violetand plaques were counted. Antiviral assays were performed by using acytopathic effect (CPE) reduction assay using vaccinia virus growing onBSC-40 cells. BSC-40 cells (40,000 per well in a microtiter dish) weregrown overnight. Lipo-IFNα1(152-189), lipo-IFNβ(150-187), orlipo-IFNτ(156-195) were added to cells at the concentrations indicatedfor 4 hr, followed by infection with BSC-40 (moi=0.1). Virus was washedafter one hr. After 48 hrs of infection, cells were stained with crystalviolet and plaques were counted. Parent IFNα1 was used at theconcentration indicated. “Scr” refers to a scrambled peptidecorresponding to IFNτ(156-195).

For FIG. 12 Showing the Protection in Mice:

Female C57BL/6 mice (6-8 weeks old) were purchased from JacksonLaboratories (Bar Harbor, Me.). For intranasal administration, vacciniavirus (10⁶ pfu) was taken in a volume of 10 μl, and 5 μl was deliveredin each of the nostrils of a lightly anesthetized mouse. Followinginfection, mice were observed daily for signs of disease, such aslethargy, ruffled hair, weight loss, and eye secretions. Moribund micewere euthanized and counted as dead.

For FIG. 13 (Weight Loss):

Mice (C57BL/6, n=3) were injected i.p. with murine IFNα1 (5×10³U/mouse), Lipo-IFNα(152-189), 5×10³ U (100 μg), or PBS, i.p. onalternate days. Activity refers to the antiviral activity assessed bycytopathic effect of EMCV on L cells. Body weight was measured onalternate days. The average body weight is presented as a percentage ofinitial weight, and the standard deviation is shown.

Following are examples that illustrate procedures for practicing theinvention. These examples should not be construed as limiting. Allpercentages are by weight and all solvent mixture proportions are byvolume unless otherwise noted.

Example 7 Type I IFN Mimetics Lack Toxicity Under Conditions whereIntact IFNs are Toxic

We compared mouse IFNβ with human IFNβ(100-187)R9 and IFNα1(69-189)R9mimetics for relative toxic effects against C57BL/6 mice as reflected byweight loss (FIG. 7). Injection of mice I.P. on alternate days with1,000 U per mouse of IFNβ resulted in approximately 15% weight loss byday 10, while mice injected with 2,000 U per mouse of IFN mimetic gainedweight as would be expected under normal growth conditions (see FIG. 7).Lymphocyte counts showed a similar pattern of toxicity with 24%reduction in IFNβ injected mice and 4-9% loss in IFN mimetic treatedmice (Table 4). A comparison of human IFNα2 with the mimetics ontoxicity/apoptosis in WISH cells showed that IFNα2 had toxicity ofapproximately 14% above controls, while the mimetics showed toxicity atthe level of untreated cells (FIG. 8). Thus, the IFN mimetics lackedtoxicity of weight loss, lymphopenia, and cellular toxicity underconditions where the intact type I IFNs were toxic.

TABLE 4 Lymphocyte suppression seen with IFN is not observed with IFNmimetics. Lymphocyte count in mice under different treatments. TreatmentLymphocytes (%) % Reduction Significance PBS 78 ± 4 IFNα(69-189)R9 75 ±3 4 NS IFNβ(100-187)R9 72 ± 5 9 NS IFNβ 59 ± 6 24 <0.01 Mice (C57BL/6, n= 3) were injected i.p. with PBS, IFN mimetics (2 × 10³ U in 200 μg permouse), or IFNβ (10³ U/mouse) on alternate days for ten days. On day 11,mice were bled. Blood smears were stained and lymphocytes were counted.

Example 8

We have synthesized three short type I IFN peptides based on ournon-canonical model of IFN signaling. If short IFNα, IFNβ, and IFNτC-terminal peptides of similar length to that of IFNγ(95-132) aresynthesized with a palmitate (lipo-) attached for cell penetration, wepredicted that they would exhibit IFN activity. We thus synthesizedhuman lipo-IFNα1(152-189) (SEQ ID NO:38), human β(150-187) (SEQ IDNO:39), ovine lipo-IFNτ(156-195) (SEQ ID NO:40), and lipo-IFNτ(156-195)scrambled (SEQ ID NO:41) as negative control and tested them variouslyfor antiviral activity, the signature property of an IFN. FIG. 9 showsthat all of the peptides except the scrambled IFNτ showed antiviralactivity against vesicular stomatitis virus (VSV). FIG. 10 gives a doseresponse of lipo-IFNα1(152-189), lipo-IFNβ(150-187), and lipo-scrambledpeptide against EMC virus. FIG. 11 gives a dose response oflipo-IFNα1(152-189), lipo-IFNβ(150-187), lipo-IFNτ(156-195), andlipo-scrambled peptides against vaccinia virus. Note that intact IFNs donot inhibit vaccinia virus, because of the virus induced decoy receptorthat blocks binding of the IFNs to receptor extracellular domain. FIG.12 shows that lipo-IFNα1(152-189) inhibited vaccinia virus lethalinfection of mice, while the intact IFNα1 and scrambled peptide wereineffective.

It should be understood that the examples and embodiments describedherein are for illustrative purposes only and that various modificationsor changes in light thereof will be suggested to persons skilled in theart and are to be included within the spirit and purview of thisapplication and the scope of the appended claims. In addition, anyelements or limitations of any invention or embodiment thereof disclosedherein can be combined with any and/or all other elements or limitations(individually or in any combination) or any other invention orembodiment thereof disclosed herein, and all such combinations arecontemplated with the scope of the invention without limitation thereto.

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We claim:
 1. An agonist peptide of a type I interferon (IFN), or apolynucleotide encoding the agonist peptide; or a polynucleotideexpression construct comprising the polynucleotide encoding the agonistpeptide; or a composition comprising the agonist peptide, thepolynucleotide, and/or the polynucleotide expression construct; whereinthe peptide does not bind to the extracellular domain of a type I IFNreceptor but does bind to the cytoplasmic domain of a type I IFNreceptor.
 2. The peptide according to claim 1, wherein the peptidecomprises the amino acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ IDNO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ ID NO:39,or SEQ ID NO:40, or a fragment thereof that exhibits substantially thesame activity as the full-length non-variant peptide, or the peptidecomprises an amino acid sequence having 60% or greater sequence identitywith the amino acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3,SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:38, SEQ ID NO:39, orSEQ ID NO:40, or a fragment thereof that exhibits substantially the sameactivity as the full-length non-variant peptide.
 3. The peptideaccording to claim 2, wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, or more amino acids are,independently, removed from and/or added to one or both termini of thepeptide.
 4. The peptide according to claim 1, wherein the peptidecomprises a protein or nucleic acid that is attached to the peptide andthat targets delivery to the cell and/or that provides for translocationof the peptide across a biological membrane of the cell.
 5. The peptideaccording to claim 1, wherein a lipophilic group is attached to thepeptide.
 6. The peptide according to claim 5, wherein the lipophilicgroup is a palmitoyl-lysine group.
 7. The peptide according to claim 5,wherein the peptide comprises one or more arginine amino acids at theN-terminus of the peptide, or at the C-terminus of the peptide, or bothtermini of the peptide.
 8. The peptide according to claim 1, wherein thepeptide comprises a nuclear localization sequence (NLS).
 9. Thecomposition according to claim 1, wherein the composition comprises asuitable carrier, diluent, or buffer.
 10. The composition according toclaim 1, wherein the composition further comprises i) one or moreantiviral compounds, and/or ii) one or more anticancer or antitumorcompounds, and/or one or more compounds for treating autoimmunedisorders.
 11. The composition according to claim 10, wherein the one ormore antiviral compound is IFNα, IFNβ, IFNγ, acyclovir (Zovirax),zidovudine (AZT), lamivudine (3TC), zanamivir (Relenza), oseltamivir(Tamiflu), valacyclovir (Valtrex), amantadine (Symmetrel), rimantadine(Flumadine), cidofovir (Vistide), foscarnet (Foscavir), ganciclovir(Cytovene), ribavirin (Virazole), nelfinavir (Viracept), ritonavir(Norvir), rifampin (Rifadin), or famciclovir (Famvir).
 12. Thecomposition according to claim 10, wherein the one or more antiviralcompounds is an interferon-gamma (IFN-γ) peptide mimetic.
 13. Thecomposition according to claim 12, wherein the IFN-γ peptide mimeticcomprises the amino acid sequence shown in SEQ ID NO:7 or SEQ ID NO:8,or a fragment thereof that exhibits substantially the same activity asthe full-length non-variant peptide.
 14. The composition according toclaim 10, wherein the one or more anticancer or antitumor compound istaxol, vinblastine, cyclophosamide, ifosfamide, 5-fluorouracil,hydroxyurea, adriamycin, bleomycin, etoposide, camptothecin,angiostatin, tamoxifen, GLEEVEC, HERCEPTIN, Bortezomib, Carfilzomib, orSalinosporamide A.
 15. The composition according to claim 1, wherein thecomposition further comprises a peptide comprising the amino acidsequence shown in SEQ ID NO:9 and/or SEQ ID NO:10, or a fragment thereofthat exhibits substantially the same activity as the full-lengthnon-variant peptide.
 16. The composition according to claim 1, whereinthe peptide or polynucleotide is encapsulated in a liposome.
 17. Thepolynucleotide expression construct according to claim 1, wherein saidexpression construct comprises one or more regulatory elements.
 18. Thepeptide according to claim 1, wherein the peptide comprises acell-penetrating peptide (CPP).
 19. The peptide according to claim 18,wherein the CPP comprises the amino acid sequence of SEQ ID NO:19; SEQID NO:20; SEQ ID NO:21; SEQ ID NO:22; SEQ ID NO:23; SEQ ID NO:24; SEQ IDNO:25; SEQ ID NO:26; SEQ ID NO:27; SEQ ID NO:28; SEQ ID NO:29; SEQ IDNO:30; SEQ ID NO:31; SEQ ID NO:32; SEQ ID NO:33; SEQ ID NO:34; SEQ IDNO:35; SEQ ID NO:36; or SEQ ID NO:37.
 20. The peptide according to claim18, wherein the CPP comprises only arginine (R) or only lysine (K) aminoacids.
 21. A kit comprising in one or more containers: i) an agonistpeptide of a type I interferon, wherein the peptide does not bind to theextracellular domain of a type I IFN receptor but does bind to thecytoplasmic domain of a type I IFN receptor; and/or ii) a polynucleotideencoding the peptide agonist; and/or iii) a polynucleotide expressionconstruct comprising the polynucleotide; and/or iv) a compositioncomprising the peptide agonist, the polynucleotide, or thepolynucleotide expression construct.
 22. An antibody, or an antigenbinding fragment thereof, that binds to an agonist peptide of a type Iinterferon, wherein the peptide does not bind to the extracellulardomain of a type I IFN receptor but does bind to the cytoplasmic domainof a type I IFN receptor.
 23. A method: a) for treating or preventinginfection by a virus in a human or animal or treating or preventing aviral associated disorder in a human or animal, said method comprisingadministering to the human or animal an effective amount of i) a peptidethat is an agonist of a type I interferon wherein the peptide does notbind to the extracellular domain of a type I IFN receptor but does bindto the cytoplasmic domain of a type I IFN receptor, or ii) apolynucleotide that encodes a peptide that is an agonist of a type Iinterferon wherein the peptide does not bind to the extracellular domainof a type I IFN receptor but does bind to the cytoplasmic domain of atype I IFN receptor, or iii) a polynucleotide expression constructcomprising the polynucleotide encoding the agonist peptide, or iv) acomposition comprising a peptide that is an agonist of a type Iinterferon wherein the peptide does not bind to the extracellular domainof a type I IFN receptor but does bind to the cytoplasmic domain of atype I IFN receptor, or a polynucleotide that encodes a peptide that isan agonist of a type I interferon wherein the peptide does not bind tothe extracellular domain of a type I IFN receptor but does bind to thecytoplasmic domain of a type I IFN receptor, or a polynucleotideexpression construct comprising the polynucleotide encoding the agonistpeptide; or b) for inducing an antiviral state in a cell against a virusor inhibiting the growth of a cancer cell, comprising contacting thecell in vitro or in vivo with an effective amount of i) a peptide thatis an agonist of a type I interferon (IFN) wherein the peptide does notbind to the extracellular domain of a type I IFN receptor but does bindto the cytoplasmic domain of a type I IFN receptor, or ii) apolynucleotide that encodes a peptide that is an agonist of a type Iinterferon (IFN) wherein the peptide does not bind to the extracellulardomain of a type I IFN receptor but does bind to the cytoplasmic domainof a type I IFN receptor, or iii) a polynucleotide expression constructcomprising the polynucleotide encoding the agonist peptide, or iv) acomposition comprising a peptide that is an agonist of a type Iinterferon wherein the peptide does not bind to the extracellular domainof a type I IFN receptor but does bind to the cytoplasmic domain of atype I IFN receptor, or a polynucleotide that encodes a peptide that isan agonist of a type I interferon wherein the peptide does not bind tothe extracellular domain of a type I IFN receptor but does bind to thecytoplasmic domain of a type I IFN receptor, or a polynucleotideexpression construct comprising the polynucleotide encoding the agonistpeptide; or c) for treating an oncological disorder or an autoimmunedisorder in a person or animal, comprising administering to the personor animal an effective amount of i) a peptide that is an agonist of atype I interferon (IFN) wherein the peptide does not bind to theextracellular domain of a type I IFN receptor but does bind to thecytoplasmic domain of a type I IFN receptor, or ii) a polynucleotidethat encodes a peptide that is an agonist of a type I interferon (IFN)wherein the peptide does not bind to the extracellular domain of a typeI IFN receptor but does bind to the cytoplasmic domain of a type I IFNreceptor, or iii) a polynucleotide expression construct comprising thepolynucleotide encoding the agonist peptide, or iv) a compositioncomprising a peptide that is an agonist of a type I interferon whereinthe peptide does not bind to the extracellular domain of a type I IFNreceptor but does bind to the cytoplasmic domain of a type I IFNreceptor, or a polynucleotide that encodes a peptide that is an agonistof a type I interferon wherein the peptide does not bind to theextracellular domain of a type I IFN receptor but does bind to thecytoplasmic domain of a type I IFN receptor, or a polynucleotideexpression construct comprising the polynucleotide encoding the agonistpeptide; or d) for activating an immune cell (e.g., T cell, NK cell,macrophage, etc.), and/or upregulating antigen presentation tolymphocytes, and/or upregulating major histocompatibility complex (MHC)molecules, and/or activating a JAK/STAT pathway, and/or activating TYK2in a cell, comprising contacting the cell in vitro or in vivo with aneffective amount of i) a peptide that is an agonist of a type Iinterferon (IFN) wherein the peptide does not bind to the extracellulardomain of a type I IFN receptor but does bind to the cytoplasmic domainof a type I IFN receptor, or ii) a polynucleotide that encodes a peptidethat is an agonist of a type I interferon (IFN) wherein the peptide doesnot bind to the extracellular domain of a type I IFN receptor but doesbind to the cytoplasmic domain of a type I IFN receptor, or iii) apolynucleotide expression construct comprising the polynucleotideencoding the agonist peptide, or iv) a composition comprising a peptidethat is an agonist of a type I interferon wherein the peptide does notbind to the extracellular domain of a type I IFN receptor but does bindto the cytoplasmic domain of a type I IFN receptor, or a polynucleotidethat encodes a peptide that is an agonist of a type I interferon whereinthe peptide does not bind to the extracellular domain of a type I IFNreceptor but does bind to the cytoplasmic domain of a type I IFNreceptor, or a polynucleotide expression construct comprising thepolynucleotide encoding the agonist peptide; or e) for inhibiting type IIFN cell activation and/or intracellular signaling, comprising providingin a cell an effective amount of an inhibitor of an interferonalpha/beta receptor (IFNAR) subunit.
 24. The method according to claim23, wherein the peptide comprises the amino acid sequence of SEQ IDNO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, or SEQ IDNO:6, SEQ ID NO:38, SEQ ID NO:39, or SEQ ID NO:40, or a fragment thereofthat exhibits substantially the same activity as the full-lengthnon-variant peptide, or the peptide comprises an amino acid sequencehaving 60% or greater sequence identity with the amino acid sequence ofSEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, or SEQID NO:6, SEQ ID NO:38, SEQ ID NO:39, or SEQ ID NO:40, or a fragmentthereof that exhibits substantially the same activity as the full-lengthnon-variant peptide.
 25. The method according to claim 23, wherein thevirus is a herpes virus, poxvirus, or picornavirus.
 26. The methodaccording to claim 23, wherein the virus is a vaccinia virus,encephalomyocarditis (EMC) virus, influenza virus, herpes simplex virus(HSV), cytomegalovirus (CMV), herpes zoster virus, and other herpesviruses, poxvirus, coxsackie virus, lentivirus, hepatitis virus(hepatitis A, B, C, D, and E), picornavirus, or vesicular stomatitisvirus (VSV).
 27. The method according to claim 26, wherein the influenzavirus is an influenza A virus.
 28. The method according to claim 27,wherein the influenza A virus is serotype H1N1.
 29. The method accordingto claim 23, wherein the peptide, polynucleotide, polynucleotideexpression construct, or composition is administered to the person oranimal prior to infection by the virus.
 30. The method according toclaim 23, wherein the peptide, polynucleotide, polynucleotide expressionconstruct, or composition is administered after the human or animal isinfected by the virus.
 31. The method according to claim 23, wherein thepeptide, polynucleotide, polynucleotide expression construct, orcomposition is administered prior to, in conjunction with, or subsequentto administration of one or more antiviral compounds.
 32. The methodaccording to claim 23, wherein the peptide, polynucleotide,polynucleotide expression construct, or composition is administered inconjunction with an interferon-gamma (IFN-γ) peptide mimetic.
 33. Themethod according to claim 31, wherein the antiviral compound is IFNα,IFNβ, IFNγ, acyclovir (Zovirax), zidovudine (AZT), lamivudine (3TC),zanamivir (Relenza), oseltamivir (Tamiflu), valacyclovir (Valtrex),amantadine (Symmetrel), rimantadine (Flumadine), cidofovir (Vistide),foscarnet (Foscavir), ganciclovir (Cytovene), ribavirin (Virazole),nelfinavir (Viracept), ritonavir (Norvir), rifampin (Rifadin), orfamciclovir (Famvir).
 34. The method according to claim 32, wherein theIFN-γ peptide mimetic comprises the amino acid sequence shown in SEQ IDNO:7 or SEQ ID NO:8, or a fragment thereof that exhibits substantiallythe same activity as the full-length non-variant peptide.
 35. The methodaccording to claim 23, wherein the peptide, polynucleotide,polynucleotide expression construct, or composition are provided in acarrier means for delivering the peptide, polynucleotide, orpolynucleotide expression construct to a cell and, optionally,facilitating transport of the peptide, polynucleotide, or polynucleotideexpression construct into the cell.
 36. The method according to claim35, wherein the carrier means comprises liposome encapsulating thepeptide, polynucleotide, polynucleotide expression construct, orcomposition.
 37. The method according to claim 35, wherein the carriermeans comprises a protein or nucleic acid that is attached to thepeptide, polynucleotide, polynucleotide expression construct, orcomposition and that targets delivery to the cell and/or that providesfor translocation of the peptide, polynucleotide, polynucleotideexpression construct, or composition across a biological membrane of thecell.
 38. The method according to claim 23, wherein a lipophilic groupis attached to the peptide.
 39. The method according to claim 38,wherein the lipophilic group is a palmitate or palmitoyl-lysine group.40. The method according to claim 38, wherein the peptide comprises oneor more arginine or lysine amino acids at the N-terminus of the peptideand/or C-terminus of the peptide.
 41. The method according to claim 23,wherein the method further comprises identifying a human or animal whois or who may be in need of treatment or prevention of infection by avirus or who is or may be in need of treatment of an oncological orautoimmune disorder.
 42. The method according to claim 23, wherein thepeptide, polynucleotide, polynucleotide expression construct, orcomposition is administered prior to, in conjunction with, or subsequentto administration of one or more anticancer or antitumor compound fortreating an oncological disorder or one or more compounds for treatingan autoimmune disorder.
 43. The method according to claim 42, whereinthe anticancer or antitumor compound is taxol, vinblastine,cyclophosamide, ifosfamide, 5-fluorouracil, hydroxyurea, adriamycin,bleomycin, etoposide, camptothecin, angiostatin, tamoxifen, GLEEVEC,HERCEPTIN, Bortezomib, Carfilzomib, or Salinosporamide A.
 44. The methodaccording to claim 23, wherein the oncological disorder is cancer and/ortumors of the anus, bile duct, bladder, bone, bone marrow, bowel(including colon and rectum), breast, eye, gall bladder, kidney, mouth,larynx, esophagus, stomach, testis, cervix, head, neck, ovary, lung,mesothelioma, neuroendocrine, penis, skin, spinal cord, thyroid, vagina,vulva, uterus, liver, muscle, pancreas, prostate, blood cells (includinglymphocytes and other immune system cells), and brain; carcinomas,Kaposi's sarcoma, melanoma, mesothelioma, soft tissue sarcoma,pancreatic cancer, lung cancer, leukemia (hairy cell, acutelymphoblastic, acute myeloid, chronic lymphocytic, chronic myeloid, andother), lymphoma (Hodgkin's and non-Hodgkin's), follicular lymphoma, ormultiple myeloma.
 45. The method according to claim 23, wherein theautoimmune disorder is multiple sclerosis or rheumatoid arthritis. 46.The peptide according to claim 1, wherein the peptide has the same orsimilar biological activity as that associated with a full-length type IIFN protein.
 47. The method according to claim 23, wherein the peptidehas the same or similar biological activity as that associated with afull-length type I IFN protein.